1308 lines
63 KiB
Promela
1308 lines
63 KiB
Promela
* \\\\ CHARMM36 All-Hydrogen Nucleic Acid Parameter File ////
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||
* Alexander D. MacKerell Jr. and coworkers
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* April 2011
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* All comments to the CHARMM web site: www.charmm.org parameter
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* set discussion forum
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||
*
|
||
|
||
!2010/2011 additions
|
||
! ejd, 2010 RNA update
|
||
! adm, 2011 DNA update
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||
! For DNA update, new atom type required for P of DNA. This required
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||
! replication of a number of parameters and the creation of new
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||
! patches, DEOX and DEO5, to convert RNA to DNA, such that previous
|
||
! CHARMM scripts to generate DNA will no longer work. Note that the
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! atom type change to P3 ONLY applies to the phosphodester linkage in
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! DNA and NOT to terminal phosphates, DMP etc.
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||
!
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||
!
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||
!references
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!
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!NUCLEIC ACIDS
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!
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||
!Hart, K., Foloppe, N., Baker, C.M., Denning, E.J., Nilsson, L. and
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!MacKerell Jr., A.D. "Optimization of the CHARMM additive force field
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||
!for DNA: Improved treatment of the BI/BII conformational
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!equilibrium," Journal of Chemical Theory and Computation, 8:348–362,
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!2012, http://dx.doi.org/10.1021/ct200723y
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||
!
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||
!Denning, E.J., Priyakumar, U.D., Nilsson, L., and MacKerell Jr., A.D.,
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||
!"Impact of 2'-hydroxyl sampling on the conformational properties of
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!RNA: Update of the CHARMM all-atom additive force field for RNA,"
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||
!JCC, In Press, 2011, NIHMSID #272247
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||
|
||
!Foloppe, N. and MacKerell, Jr., A.D. "All-Atom Empirical Force Field for
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!Nucleic Acids: 1) Parameter Optimization Based on Small Molecule and
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!Condensed Phase Macromolecular Target Data. JCC, 2000, 21: 86-104.
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||
!
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!MacKerell, Jr., A.D. and Banavali, N. "All-Atom Empirical Force Field for
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!Nucleic Acids: 2) Application to Molecular Dynamics Simulations of DNA
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!and RNA in Solution. JCC, 2000, 21: 105-120.
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!
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ATOMS
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MASS -1 HN1 1.00800 ! Nucleic acid amine proton
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MASS -1 HN2 1.00800 ! Nucleic acid ring nitrogen proton
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MASS -1 HN3 1.00800 ! Nucleic acid aromatic carbon proton
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||
MASS -1 HN4 1.00800 ! Nucleic acid phosphate hydroxyl proton
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||
MASS -1 HN5 1.00800 ! Nucleic acid ribose hydroxyl proton
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||
MASS -1 HN6 1.00800 ! Nucleic acid ribose aliphatic proton
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||
MASS -1 HN7 1.00800 ! Nucleic acid proton (equivalent to protein HA)
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||
MASS -1 HN8 1.00800 ! Bound to CN8 in nucleic acids/model compounds
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MASS -1 HN9 1.00800 ! Bound to CN9 in nucleic acids/model compounds
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||
MASS -1 CN1 12.01100 ! Nucleic acid carbonyl carbon
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||
MASS -1 CN1T 12.01100 ! Nucleic acid carbonyl carbon (T/U C2)
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MASS -1 CN2 12.01100 ! Nucleic acid aromatic carbon to amide
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MASS -1 CN3 12.01100 ! Nucleic acid aromatic carbon
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||
MASS -1 CN3T 12.01100 ! Nucleic acid aromatic carbon, Thy C5
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MASS -1 CN4 12.01100 ! Nucleic acid purine C8 and ADE C2
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||
MASS -1 CN5 12.01100 ! Nucleic acid purine C4 and C5
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MASS -1 CN5G 12.01100 ! Nucleic acid guanine C5
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||
MASS -1 CN7 12.01100 ! Nucleic acid carbon (equivalent to protein CT1)
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||
MASS -1 CN7B 12.01100 ! Nucleic acid aliphatic carbon for C1'
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||
MASS -1 CN8 12.01100 ! Nucleic acid carbon (equivalent to protein CT2)
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MASS -1 CN8B 12.01100 ! Nucleic acid carbon (equivalent to protein CT2)
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MASS -1 CN9 12.01100 ! Nucleic acid carbon (equivalent to protein CT3)
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MASS -1 NN1 14.00700 ! Nucleic acid amide nitrogen
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MASS -1 NN2 14.00700 ! Nucleic acid protonated ring nitrogen
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MASS -1 NN2B 14.00700 ! From NN2, for N9 in GUA different from ADE
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MASS -1 NN2U 14.00700 ! Nucleic acid protonated ring nitrogen, ura N3
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MASS -1 NN2G 14.00700 ! Nucleic acid protonated ring nitrogen, gua N1
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||
MASS -1 NN3 14.00700 ! Nucleic acid unprotonated ring nitrogen
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MASS -1 NN3A 14.00700 ! Nucleic acid unprotonated ring nitrogen, ade N1 and N3
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MASS -1 NN3G 14.00700 ! Nucleic acid unprotonated ring nitrogen, gua N3
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||
MASS -1 NN4 14.00700 ! Nucleic acid purine N7
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MASS -1 NN6 14.00700 ! Nucleic acid sp3 amine nitrogen (equiv to protein nh3)
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||
MASS -1 ON1 15.99940 ! Nucleic acid carbonyl oxygen
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||
MASS -1 ON1C 15.99940 ! Nucleic acid carbonyl oxygen, cyt O2
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MASS -1 ON2 15.99940 ! Nucleic acid phosphate ester oxygen
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MASS -1 ON3 15.99940 ! Nucleic acid =O in phosphate
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MASS -1 ON4 15.99940 ! Nucleic acid phosphate hydroxyl oxygen
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MASS -1 ON5 15.99940 ! Nucleic acid ribose hydroxyl oxygen
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MASS -1 ON6 15.99940 ! Nucleic acid deoxyribose ring oxygen
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MASS -1 ON6B 15.99940 ! Nucleic acid ribose ring oxygen
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MASS -1 P 30.97400 ! phosphorus
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MASS -1 P2 30.97400 ! phosphorus, adm, 2011 DNA update
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MASS -1 P3 30.97400 ! pyrophosphate phosphorus
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MASS -1 P4 30.97400 ! protonated pyrophosphate phosphorus
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BONDS
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!
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!V(bond) = Kb(b - b0)**2
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!
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!Kb: kcal/mole/A**2
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!b0: A
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!
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!atom type Kb b0
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!
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||
!2-(aminobutyl)-1,3-propandiol terms
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CN8 NN6 200.000 1.480 ! methylammonium
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NN6 HN1 403.000 1.040 ! methylammonium
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!abasic deoxynucleoside
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ON6 CN8B 260.0 1.420 ! susil
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CN8 CN8B 222.50 1.528 ! Alkanes, sacred
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!
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CN1 CN3 302.0 1.409 !U, adm jr. 11/97
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CN1 CN3T 302.0 1.403 !T, adm jr. 11/97
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CN1 CN5G 302.0 1.360 !G, adm jr. 11/97
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CN1 NN2 380.0 1.367 !C, adm jr. 11/97
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CN1T NN2B 302.0 1.348 !U,T adm jr. 11/97
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||
CN1 NN2G 340.0 1.396 !G, adm jr. 11/97
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CN1 NN2U 340.0 1.389 !U,T adm jr. 11/97
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CN1T NN2U 340.0 1.383 !U,T adm jr. 11/97
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CN1 NN3 350.0 1.335 !C, adm jr. 11/97
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CN1T ON1 860.0 1.230 !nad/ppi, jjp1/adm jr. 7/95
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CN1 ON1 660.0 1.234 !U,A,G par_a4 adm jr. 10/2/91
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CN1 ON1C 620.0 1.245 !C, adm jr. 10/2/91
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CN2 CN3 320.0 1.406 !C, adm jr. 11/97
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CN2 CN5 360.0 1.358 !A, adm jr. 11/97
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CN2 NN1 360.0 1.366 !C,A,G JWK, adm jr. 10/2/91
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CN2 NN2G 400.0 1.392 !G
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CN2 NN3 450.0 1.343 !C
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CN2 NN3A 400.0 1.342 !A, adm jr. 11/97
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CN2 NN3G 320.0 1.326 !G, adm jr. 11/97
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CN3 CN3 500.0 1.326 !C,U adm jr. 11/97
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CN3 CN3T 560.0 1.320 !T, adm jr. 11/97
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CN3T CN9 230.0 1.478 !T, adm jr. 11/97
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CN3 HN3 350.0 1.09 !C,U, JWK
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CN3T HN3 350.0 1.09 !T, JWK
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CN3 NN2 302.0 1.343 !C, adm jr. 11/97
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CN3 NN2B 320.0 1.343 !U,T adm jr. 11/97
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CN4 HN3 380.0 1.09 !G,A, JWK par_a7 9/30/91
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CN4 NN2 320.0 1.374 !A, adm jr. 11/97
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CN4 NN2B 300.0 1.378 !G, adm jr. 11/97
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CN4 NN3A 420.0 1.322 !A, adm jr. 11/97
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CN4 NN4 400.0 1.305 !G,A, adm jr. 11/97
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CN5 CN5 310.0 1.361 !A, adm jr. 11/97
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CN5 CN5G 320.0 1.350 !G, adm jr. 11/97
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CN5 NN2 300.0 1.375 !A, adm jr. 11/97
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CN5 NN2B 302.0 1.375 !G, adm jr. 11/97
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CN5 NN3A 350.0 1.312 !A, JWK par_a8 9/30/91
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CN5 NN3G 350.0 1.315 !G, adm jr. 11/97
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CN5 NN4 310.0 1.355 !A, adm jr. 11/97
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CN5G NN4 310.0 1.365 !G, adm jr. 11/97
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CN8 CN8 222.50 1.528 !Alkanes, sacred
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||
CN8 CN9 222.50 1.528 !Alkanes, sacred
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CN8 NN2 400.0 1.460 !9-E-GUA, ADM JR.
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CN8 ON5 428.0 1.42 !RIBOSE, MeOH
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CN9 HN9 322.0 1.111 !alkanes
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CN9 ON2 340.0 1.43 !DMP, ADM Jr.
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HN1 NN1 488.0 1.00 !A,C,G, JWK, adm jr. 7/24/91
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HN2 NN2 474.0 1.01 !C,U, JWK
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HN2 NN2B 474.0 1.01 !G, adm jr. 11/97
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HN2 NN2G 471.0 1.01 !G, JWK, par_a12 9/30/91
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HN2 NN2U 474.0 1.01 !U, JWK, adm jr. 7/24/91
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HN4 ON4 545.0 0.960 !MP_1, ADM Jr.
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ON2 P 270.0 1.60 !DMP, ADM Jr.
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ON2 P2 270.0 1.60 !DMP, ADM Jr., adm, 2011 DNA update
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ON3 P 580.0 1.48 !DMP, ADM Jr.
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ON3 P2 580.0 1.48 !DMP, ADM Jr., adm, 2011 DNA update
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ON4 P 237.0 1.58 !MP_1, ADM Jr.
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ON4 P2 237.0 1.58 !MP_1, ADM Jr., adm, 2011 DNA update
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!NN5 HN1 460.0 1.01 !sugar model, adm jr.
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!@@@@@@@@@ Begining of endocyclic bonds for deoxy-ribose @@@@@@@@@
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CN7B ON6 260.0 1.420 ! From exp
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CN7B CN8 200.0 1.518 ! From exp
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||
CN7 ON6 240.0 1.446 ! Fom exp.
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||
CN7 CN7 222.5 1.529 ! From exp
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CN7 CN8 222.5 1.516 ! From exp.
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CN7 CN9 222.5 1.516 ! for 5MET, From alkanes
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CN7 HN7 309.0 1.111 !Alkanes, sacred
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||
CN8 HN8 309.0 1.111 !Alkanes, sacred
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||
CN7B HN7 309.0 1.111 ! From CN8 HN7 (NF)
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!@@@@@@@@@ End of endocyclic bonds for deoxy-ribose @@@@@@@@@
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!@@@@@@@@@ Begining of endocyclic bonds for ribose @@@@@@@@@
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||
CN7B ON6B 260.0 1.420 ! From CN7B ON6
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||
CN7 ON6B 240.0 1.480 ! From CN7 ON6
|
||
CN7B CN7B 200.0 1.450 !
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||
CN7 CN7B 222.5 1.460 ! Specific to RNA
|
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!@@@@@@@@@ End of endocyclic bonds for ribose @@@@@@@@@
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||
|
||
!@@@@@@@@@ Begining of exocyclic bonds for deoxy-ribose @@@@@@@@@
|
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CN7 CN8B 222.5 1.512 ! From exp.
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||
CN8B ON2 320.0 1.44 ! From exp
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||
!CN8B ON5 250.0 1.44 ! From CN8B ON2
|
||
CN8B ON5 428.0 1.42 !From CN8 ON2, adm jr., 8/30/98
|
||
CN7 ON2 310.0 1.433 ! From exp
|
||
CN7B ON2 310.0 1.433 ! From exp, for NADPH and bkbmod
|
||
!CN7 ON5 250.0 1.420 ! ALLOW ALI ALC ARO
|
||
CN7 ON5 428.0 1.42 !From CN8 ON2, adm jr., 8/30/98
|
||
! C1'-N9 (purines)/C1'-N1 (pyrimidines)
|
||
CN9 NN2 400.0 1.456 !9-M-A/C, adm jr.
|
||
CN8 NN2B 400.0 1.458 !9-M-G/T/U, adm jr.
|
||
CN9 NN2B 400.0 1.458 !9-M-G/T/U, adm jr.
|
||
CN7B NN2 220.0 1.456 !A/C
|
||
CN7B NN2B 220.0 1.458 !G/T/U
|
||
! C5'-H in model compounds and DNA
|
||
CN8B HN8 309.0 1.111 !Alkanes, sacred
|
||
ON5 HN5 545.0 0.960 !RIBOSE, MeOH
|
||
!@@@@@@@@@ End of exocyclic bonds for deoxy-ribose @@@@@@@@@
|
||
|
||
!@@@@@@@@@ Begining of exocyclic bonds for ribose @@@@@@@@@
|
||
!CN7B ON5 250.0 1.400 ! From CN7 ON5
|
||
CN7B ON5 428.0 1.400 ! check adm jr.,
|
||
!FC should be 428.000 based on Meoh
|
||
!@@@@@@@@@ End of exocyclic bonds for ribose @@@@@@@@@
|
||
|
||
!@@@@@@@@@ Begining of bonds for nucleotide analogue @@@@@@@@@
|
||
CN8 ON2 340.0 1.44 !
|
||
!@@@@@@@@@ End of bonds for nucleotide analogue @@@@@@@@@
|
||
!from nad_ppi stream file
|
||
ON2 P3 300.0 1.68 !nad/ppi, jjp1/adm jr. 7/95
|
||
ON3 P3 480.0 1.53 !nad/ppi, jjp1/adm jr. 7/95
|
||
ON2 P4 300.0 1.68 !PPI2, from nad/ppi, adm jr. 7/01
|
||
ON3 P4 480.0 1.53 !PPI2, from nad/ppi, adm jr. 7/01
|
||
ON4 P4 237.0 1.58 !PPI2, from MP_1, ADM Jr.
|
||
|
||
ANGLES
|
||
!
|
||
!V(angle) = Ktheta(Theta - Theta0)**2
|
||
!
|
||
!V(Urey-Bradley) = Kub(S - S0)**2
|
||
!
|
||
!Ktheta: kcal/mole/rad**2
|
||
!Theta0: degrees
|
||
!Kub: kcal/mole/A**2 (Urey-Bradley)
|
||
!S0: A
|
||
!
|
||
!atom types Ktheta Theta0 Kub S0
|
||
!
|
||
! angle parameters have been rearranged based on model
|
||
! compounds and functional groups. Additional angle
|
||
! parameters follow sorted based on the central atom
|
||
!
|
||
!2-(aminobutyl)-1,3-propandiol terms
|
||
CN7 CN8 CN8 58.35 113.60 11.16 2.561 !alkane
|
||
CN8 CN7 CN8 58.35 113.60 11.16 2.561 !alkane
|
||
CN8 CN8 CN8 58.35 113.60 11.16 2.561 !alkane
|
||
HN1 NN6 CN8 30.00 109.50 20.00 2.074 !methylammonium
|
||
NN6 CN8 HN8 45.00 107.50 35.00 2.101 !methylammonium
|
||
CN7 CN8 ON2 115.00 109.70 !DNA exocyclic angles
|
||
NN6 CN8 CN8 67.70 110.00 !methylammonium
|
||
HN1 NN6 HN1 44.00 109.50 !methylammonium
|
||
!abasic propyl linkage
|
||
ON2 CN8 CN8 115.0 109.7 !DNA exocyclic angles
|
||
!abasic deoxynucleoside
|
||
CN7 ON6 CN8B 110.0 109.0
|
||
ON6 CN8B CN8 90.0 106.0
|
||
CN8B CN8 CN7 80.0 106.0
|
||
ON6 CN8B HN8 45.2 107.24 !
|
||
HN8 CN8B CN8 34.53 110.10 22.53 2.179 ! alkane
|
||
HN8 CN8 CN8B 34.53 110.10 22.53 2.179 ! alkane
|
||
|
||
! pyrmidines
|
||
!@@@@@@@@ Adenine
|
||
! ade 6-mem ring
|
||
CN2 NN3A CN4 90.0 117.8 !6R) adm jr. 11/97
|
||
NN3A CN4 NN3A 60.0 133.0 !6R)
|
||
CN4 NN3A CN5 90.0 110.1 !6R)
|
||
CN5 CN5 NN3A 60.0 127.4 !6R) bridgeC4
|
||
CN2 CN5 CN5 60.0 121.0 !6R) bridgeC5
|
||
CN5 CN2 NN3A 60.0 110.7 !6R)
|
||
CN5 CN5 NN2 100.0 105.7 !5R) bridgeC4
|
||
CN5 CN5 NN4 100.0 110.0 !5R) bridgeC5
|
||
CN4 NN4 CN5 120.0 104.6 !5R)
|
||
NN2 CN4 NN4 100.0 113.4 !5R)
|
||
CN4 NN2 CN5 100.0 106.3 !5R)
|
||
NN2 CN5 NN3A 100.0 126.9 !bridgeC4
|
||
CN2 CN5 NN4 100.0 129.0 !bridgeC5
|
||
HN3 CN4 NN3A 38.0 113.5 !h2
|
||
NN3A CN2 NN1 50.0 130.7 !n6
|
||
CN5 CN2 NN1 50.0 118.6 !
|
||
CN2 NN1 HN1 40.0 121.5 !h61,h62, C,A,G
|
||
HN1 NN1 HN1 31.0 117.0 !C,A,G
|
||
NN4 CN4 HN3 39.0 124.8 !h8, G,A
|
||
NN2 CN4 HN3 39.0 121.8 !
|
||
CN5 NN2 HN2 30.0 129.4 !h9
|
||
CN4 NN2 HN2 30.0 125.0 !
|
||
!@@@@@@@@ Guanine
|
||
! gua 6-mem ring
|
||
CN1 NN2G CN2 70.0 131.1 !6R)G, adm jr. 11/97
|
||
NN2G CN2 NN3G 70.0 122.2 !6R)
|
||
CN2 NN3G CN5 90.0 109.4 !6R)
|
||
CN5G CN5 NN3G 70.0 129.9 !6R) bridgeC4
|
||
CN1 CN5G CN5 70.0 119.6 !6R) bridgeC5
|
||
CN5G CN1 NN2G 70.0 107.8 !6R)
|
||
CN5G CN5 NN2B 100.0 104.6 !5R) bridgeC4
|
||
CN5 CN5G NN4 100.0 111.4 !5R) bridgeC5
|
||
CN4 NN4 CN5G 120.0 103.8 !5R)
|
||
NN2B CN4 NN4 100.0 113.0 !5R)
|
||
CN4 NN2B CN5 100.0 107.2 !5R)
|
||
NN2B CN5 NN3G 140.0 125.5 ! bridgeC4
|
||
CN1 CN5G NN4 125.0 129.0 ! bridgeC5
|
||
CN1 NN2G HN2 45.0 113.3 ! h1
|
||
CN2 NN2G HN2 45.0 115.6 !
|
||
NN1 CN2 NN2G 95.0 115.4 ! n2
|
||
NN1 CN2 NN3G 95.0 122.4 !
|
||
NN2G CN1 ON1 50.0 127.5 ! o6
|
||
CN5G CN1 ON1 50.0 124.7 !
|
||
HN3 CN4 NN2B 40.0 122.2 ! h8 (NN4 CN4 HN3 124.8)
|
||
CN4 NN2B HN2 30.0 124.6 ! h9
|
||
CN5 NN2B HN2 30.0 129.3 !
|
||
!@@@@@@@@ Cytosine
|
||
! cyt 6-mem ring
|
||
CN1 NN2 CN3 50.0 124.1 !C, adm jr. 11/97
|
||
NN2 CN1 NN3 50.0 116.8 !C
|
||
CN1 NN3 CN2 85.0 119.1 !C
|
||
CN3 CN2 NN3 85.0 119.3 !C
|
||
CN2 CN3 CN3 85.0 117.8 !C
|
||
CN3 CN3 NN2 85.0 122.9 !C
|
||
CN1 NN2 HN2 37.0 121.2 !C, h1
|
||
CN3 NN2 HN2 37.0 114.7 !C
|
||
NN2 CN1 ON1C 130.0 119.4 !C, o2
|
||
NN3 CN1 ON1C 130.0 123.8 !C
|
||
NN3 CN2 NN1 81.0 122.3 !C, n4
|
||
CN3 CN2 NN1 81.0 118.4 !C
|
||
CN2 CN3 HN3 38.0 120.1 !C h5
|
||
CN3 CN3 HN3 38.0 122.1 !C,U
|
||
HN3 CN3 NN2 44.0 115.0 !C, h6
|
||
!@@@@@@@@ Uracil
|
||
! ura 6-mem ring
|
||
CN1T NN2B CN3 70.0 122.0 !U, adm jr. 11/97
|
||
NN2B CN1T NN2U 50.0 114.0 !U
|
||
CN1T NN2U CN1 50.0 130.2 !U
|
||
NN2U CN1 CN3 70.0 112.6 !U
|
||
CN1 CN3 CN3 100.0 117.6 !U
|
||
CN3 CN3 NN2B 100.0 123.6 !U
|
||
CN1T NN2B HN2 40.5 122.0 !U, h1
|
||
CN3 NN2B HN2 32.0 116.0 !U
|
||
NN2B CN1T ON1 100.0 121.6 !U, o2
|
||
NN2U CN1T ON1 100.0 124.4 !U
|
||
CN1T NN2U HN2 40.5 114.4 !U, h3
|
||
CN1 NN2U HN2 40.5 115.4 !U
|
||
NN2U CN1 ON1 100.0 121.9 !U, o4
|
||
CN3 CN1 ON1 100.0 125.5 !U,
|
||
CN1 CN3 HN3 30.0 120.3 !U, h5
|
||
HN3 CN3 NN2B 30.0 114.3 !U, h6
|
||
! thymine 6-mem ring (unique from ura)
|
||
CN3T CN1 NN2U 70.0 113.5 !T, adm jr. 11/97
|
||
CN1 CN3T CN3 120.0 116.7 !T
|
||
CN3T CN3 NN2B 120.0 123.6 !125.3 !T
|
||
CN3T CN1 ON1 100.0 124.6 !T, o4
|
||
CN1 CN3T CN9 38.0 118.7 !T, c5 methyl
|
||
CN3 CN3T CN9 38.0 124.6 !T
|
||
CN3T CN3 HN3 30.0 122.1 !T, h6
|
||
! base to methyl connection
|
||
CN1T NN2B CN9 70.0 116.0 !1-M-T/U, adm jr.
|
||
CN3 NN2B CN9 70.0 122.0 !1-M-T/U, adm jr. 7/24/91
|
||
CN1 NN2 CN9 70.0 115.4 !1-M-C, adm jr.
|
||
CN3 NN2 CN9 70.0 120.5 !1-M-C, adm jr. 7/24/91
|
||
CN5 NN2 CN9 70.0 125.9 !9-M-A, adm jr.
|
||
CN4 NN2 CN9 70.0 127.8 !9-M-A, adm jr.
|
||
CN5 NN2B CN9 70.0 125.9 !9-M-G, adm jr.
|
||
CN4 NN2B CN9 70.0 126.9 !9-M-G, adm jr.
|
||
CN5 NN2B CN8 70.0 125.9 !9-E-G, adm jr.
|
||
CN4 NN2B CN8 70.0 126.9 !9-E-G, adm jr.
|
||
NN2B CN8 CN9 70.0 113.7 !9-E-G, adm jr.
|
||
!===== For glycosydic linkage, base to c1'
|
||
CN1T NN2B CN7B 45.0 118.4 !U/T, FC from A
|
||
CN3 NN2B CN7B 45.0 119.6 !U/T
|
||
CN1 NN2 CN7B 45.0 120.0 !C, FC from A
|
||
CN3 NN2 CN7B 45.0 115.9 !C
|
||
CN5 NN2 CN7B 45.0 126.1 !A
|
||
CN4 NN2 CN7B 45.0 127.6 !A
|
||
CN5 NN2B CN7B 45.0 126.5 !G
|
||
CN4 NN2B CN7B 45.0 126.3 !G
|
||
ON6 CN7B NN2 110.0 108.0 !C/A DNA
|
||
ON6B CN7B NN2 110.0 112.0 !C/A RNA
|
||
CN8 CN7B NN2 110.0 113.7 !C/A
|
||
CN7B CN7B NN2 110.0 111.0 !C/A, RNA
|
||
ON6 CN7B NN2B 110.0 108.0 !T/U/G (DNA) FC from A
|
||
ON6B CN7B NN2B 110.0 112.0 !T/U/G (RNA) FC from A
|
||
CN8 CN7B NN2B 110.0 113.7 !T/U/G
|
||
CN7B CN7B NN2B 110.0 111.0 !T/U/G, RNA
|
||
HN7 CN7B NN2 43.0 111.0 !
|
||
HN7 CN7B NN2B 43.0 111.0 !From HN7 CN7B NN2
|
||
!===== End of glycosydic linkage
|
||
! remaining terms ordered based on central atom
|
||
CN9 CN8 HN8 34.6 110.10 22.53 2.179 ! Alkanes, sacred
|
||
CN9 CN7 HN7 34.6 110.10 22.53 2.179 ! Alkanes, sacred
|
||
HN8 CN8 NN2 33.43 110.1 !FOR 9-M-ADE(THY), ADM
|
||
HN8 CN8 ON5 45.9 108.89 !RIBOSE, Adm Jr. MeOH
|
||
CN3 CN9 HN9 33.43 110.10 22.53 2.179 ! Alkanes, sacred
|
||
CN3T CN9 HN9 33.43 110.10 22.53 2.179 ! Alkanes, sacred
|
||
CN8 CN9 HN9 34.60 110.10 22.53 2.179 ! Alkanes, sacred
|
||
HN9 CN9 CN7 33.43 110.1 22.53 2.179 ! Alkanes, sacred
|
||
HN9 CN9 NN2 33.43 110.1 !FOR 9-M-A(T), adm jr.
|
||
HN9 CN9 NN2B 33.43 110.1 !FOR 9-M-G(C), adm jr.
|
||
HN8 CN8 NN2B 33.43 110.1 !FOR 9-E-G, adm jr.
|
||
HN9 CN9 ON2 60.0 109.5 !DMP, ADM Jr.
|
||
!HN1 NN5 HN1 39.0 106.0 ! sugar model, adm jr.
|
||
CN9 ON2 P 20.0 120.0 35. 2.33 !DMP, ADM Jr.
|
||
HN4 ON4 P 30.0 115.0 40.0 2.35 !MP_1, ADM Jr.
|
||
HN4 ON4 P2 30.0 115.0 40.0 2.35 !MP_1, ADM Jr. , adm, 2011 DNA update
|
||
HN5 ON5 CN8 57.5 106.0 !RIBOSE, Adm Jr. MeOH
|
||
HN5 ON5 CN9 57.5 106.0 !RIBOSE, Adm Jr. MeOH
|
||
ON2 P ON2 80.0 104.3 !DMP, ADM Jr.
|
||
ON2 P2 ON2 80.0 104.3 !DMP, ADM Jr., adm, 2011 DNA update
|
||
ON2 P ON4 48.1 108.0 !MP_1, ADM Jr.
|
||
ON2 P2 ON4 48.1 108.0 !MP_1, ADM Jr., adm, 2011 DNA update
|
||
ON3 P ON4 98.9 108.23 !MP_1, ADM Jr.
|
||
ON3 P2 ON4 98.9 108.23 !MP_1, ADM Jr., adm, 2011 DNA update
|
||
ON4 P ON4 98.9 104.0 !MP_0, ADM Jr.
|
||
ON4 P2 ON4 98.9 104.0 !MP_0, ADM Jr., adm, 2011 DNA update
|
||
CN7 CN8 ON5 75.7 110.10 !RIBOSE, adm jr. MeOH
|
||
HN9 CN9 HN9 35.500 108.40 5.40 1.802 !alkane update, adm jr. 3/2/92
|
||
!@@@@@@@@@ Beginning of endocyclic valence angles for regular DNA @@@@@@@
|
||
CN7 ON6 CN7B 110.0 108.0 ! NF, 11/97, C4'O4'C1'
|
||
ON6 CN7B CN8 90.0 102.0 ! NF, 11/97, C4'O4'C1'
|
||
CN7B CN8 CN7 80.00 100.0 ! NF, 11/97, C1'C2'C3'
|
||
CN8 CN7 CN7 60.00 102.0 8.0 2.561 !NF, 11/97, C2'C3'C4'
|
||
CN9 CN7 CN7 60.00 102.0 8.0 2.561 !for 5MET, adm jr.
|
||
CN7 CN7 ON6 100.0 104.0 ! NF, 11/97, C3'C4'O4'
|
||
HN7 CN7 ON6 45.2 107.24 !
|
||
HN7 CN7B ON6 45.2 107.24 !
|
||
HN7 CN7 CN7 40.0 108.00 !
|
||
CN7B CN8 HN8 33.4 110.10 22.53 2.179 ! following terms directly
|
||
CN8 CN7B HN7 33.4 110.10 22.53 2.179 ! from alkanes
|
||
HN7 CN7 CN8 34.5 110.1 22.53 2.179 !
|
||
HN8 CN8 CN7 34.53 110.10 22.53 2.179 !
|
||
HN8 CN8 CN8 34.53 110.10 22.53 2.179 !
|
||
HN8 CN8 HN8 35.5 109.00 5.40 1.802 !
|
||
HN7 CN7 HN7 35.5 109.00 5.40 1.802 !
|
||
!@@@@@@@@@ End of endocyclic valence angles for regular DNA @@@@@@@
|
||
|
||
!@@@@@@@@@ Beginning of endocyclic valence angles for regular RNA @@@@@@@
|
||
CN7 ON6B CN7B 110.0 115.0 ! From CN7 ON6 CN7B
|
||
CN7 CN7 ON6B 100.0 110.0 ! From CN7 CN7 ON6
|
||
ON6B CN7B CN7B 90.0 106.0 ! 030998
|
||
CN7B CN7B CN7 110.0 96.0 !
|
||
CN7B CN7 CN7 60.0 100.0 8.00 2.561 !NF, 11/97, C2'C3'C4'
|
||
HN7 CN7 ON6B 45.2 107.24 !
|
||
HN7 CN7B ON6B 45.2 107.24 !
|
||
CN7B CN7B HN7 33.4 110.10 22.53 2.179 ! following terms directly
|
||
HN7 CN7B HN7 35.5 109.00 5.40 1.802 !
|
||
!@@@@@@@@@ End of endocyclic valence angles for regular RNA @@@@@@@
|
||
|
||
!@@@@@@@@@ Beginning of exocyclic valence angles for regular DNA @@@@@@@
|
||
ON6 CN7 CN8B 90.0 108.2 !NF, 11/97, O4'C4'C5'
|
||
ON6 CN7 CN9 90.0 108.2 !for 5MET, adm jr.
|
||
CN7 CN7 CN8B 45.0 110.0 !NF, 11/97, C3'C4'C5'
|
||
CN8 CN7 CN8B 58.35 113.60 11.16 2.561 ! from alkane, 25P1
|
||
CN7 CN8B ON2 70.0 108.4 !NF, 11/97, C4'C5'O5'
|
||
CN7 CN7 ON2 115.0 109.7 !NF, 11/97, C4'C3'O3'
|
||
CN7B CN7B ON2 115.0 109.7 !NF, 11/97, C4'C3'O3' for NADPH and bkbmod
|
||
CN8 CN7 ON2 115.0 109.7 !NF, 11/97, C2'C3'O3'
|
||
CN8B ON2 P 20.0 120.0 35.00 2.33 !NF, 11/97, C5'O5'P
|
||
CN8B ON2 P2 20.0 120.0 35.00 2.33 !NF, 11/97, C5'O5'P, adm, 2011 DNA update
|
||
CN7 ON2 P 20.0 120.0 35.00 2.33 !NF, 11/97, C3'O3'P
|
||
CN7 ON2 P2 20.0 120.0 35.00 2.33 !NF, 11/97, C3'O3'P, adm, 2011 DNA update
|
||
CN7B ON2 P 20.0 120.0 35.00 2.33 !NF, 11/97, C3'O3'P, for NADPH and bkbmod
|
||
CN7B ON2 P2 20.0 120.0 35.00 2.33 !NF, 11/97, C3'O3'P, for NADPH and bkbmod, adm, 2011 DNA update
|
||
! sugar
|
||
HN7 CN7 CN8B 34.5 110.1 22.53 2.179 ! From HN7 CN7 CN8
|
||
HN8 CN8B ON2 60.0 109.5 ! From HN7 CN8 ON2
|
||
HN5 ON5 CN8B 57.5 106.0 ! From HN5 ON5 CN8
|
||
HN8 CN8B HN8 35.5 109.0 5.40 1.802 ! Alkanes, sacred
|
||
HN8 CN8B CN7 34.53 110.1 22.53 2.179 ! Alkanes, sacred
|
||
HN7 CN7 ON2 60.0 109.5 !DMP, adm jr. from HN7 CN8 ON2
|
||
HN7 CN7B ON2 60.0 109.5 !DMP, adm jr. from HN7 CN8 ON2, for NADPH and bkbmod
|
||
!===== For 5ter patch:
|
||
CN7 CN8B ON5 75.7 110.10 ! From CN7 CN8B ON5
|
||
CN8B CN7 ON5 90.0 108.2 ! phosphoramidate, carbocyclic
|
||
HN8 CN8B ON5 45.9 108.89 ! From HN7 CN8 ON5
|
||
!===== For 3ter patch:
|
||
ON5 CN7 CN8 75.7 110.0 ! from CHARMM22
|
||
ON5 CN7 CN7 75.7 110.1 !
|
||
HN7 CN7 ON5 60.0 109.5 !
|
||
HN5 ON5 CN7 57.5 109.0 !
|
||
!@@@@@@@@@ End of exocyclic valence angles for regular DNA @@@@@@@
|
||
|
||
!@@@@@@@@@ Beginning of exocyclic valence angles for regular RNA @@@@@@@
|
||
!O4'-C4'-C5'
|
||
ON6B CN7 CN8B 90.0 108.2 !
|
||
ON6B CN7 CN9 90.0 108.2 ! for 5MET patch, adm jr.
|
||
!O3'-C3'-C2'
|
||
ON2 CN7 CN7B 90.0 110.0 !
|
||
ON5 CN7 CN7B 90.0 110.0 ! From ON5 CN7 CN8
|
||
!O2'-C2'-C1'
|
||
ON5 CN7B CN7B 80.0 108.4 !
|
||
!O2'-C2'-C3'
|
||
ON5 CN7B CN7 90.0 108.0 !
|
||
HN7 CN7B ON5 60.0 109.5 !
|
||
HN5 ON5 CN7B 57.5 109.0 !
|
||
HN7 CN7B CN7 34.53 110.10 22.53 2.179
|
||
HN7 CN7 CN7B 34.53 110.10 22.53 2.179
|
||
|
||
!@@@@@@@@@ End of exocyclic valence angles for regular RNA @@@@@@@
|
||
|
||
!@@@@@@@@@ Beginning of angles for the nucleotide analogue @@@@@@@
|
||
CN8 ON2 P 20.0 120.0 35. 2.33 !DMP, adm jr.
|
||
CN8 ON2 P2 20.0 120.0 35. 2.33 !DMP, adm jr., adm 2011 DNA update
|
||
!@@@@@@@@@ End of angles for the nucleotide analogue @@@@@@@
|
||
ON2 P ON3 98.9 111.6 !DMP, adm jr.
|
||
ON2 P2 ON3 98.9 111.6 !DMP, adm jr., adm, 2011 DNA update
|
||
ON3 P ON3 120.0 120.0 !DMP, adm jr.
|
||
ON3 P2 ON3 120.0 120.0 !DMP, adm jr., adm, 2011 DNA update
|
||
HN8 CN8 ON2 60.0 109.5 !DMP, adm jr.
|
||
ON5 P ON3 98.9 111.6 ! From ON2 P ON3
|
||
!------------------------ added for araim ----------------------
|
||
ON6 CN7B CN7 120.0 106.25 !
|
||
CN7B CN7 CN8 58.35 113.6 11.16 2.561 !
|
||
!from nad_ppi stream file
|
||
P ON2 P 15.0 140.0 -40.0 2.80 !nad/ppi, jjp1/adm jr. 7/95
|
||
CN9 ON2 P3 20.0 120.0 35. 2.33 !nad/ppi, jjp1/adm jr. 7/95
|
||
P3 ON2 P 15.0 140.0 -40.0 2.80 !nad/ppi, jjp1/adm jr. 7/95
|
||
P4 ON2 P 45.0 140.0 40.0 3.15 !PPI2, from nad/ppi, adm jr., 7/01
|
||
P3 ON2 P3 15.0 140.0 -40.0 2.80 !nad/ppi, jjp1/adm jr. 7/95
|
||
HN4 ON4 P4 30.0 120.0 40.0 2.35 !PPI2, from MP_1, adm jr., 7/01
|
||
ON2 P4 ON4 48.1 100.0 !PPI2, from MP_1, adm jr., 7/01
|
||
ON3 P4 ON4 98.9 108.23 !PPI2, from MP_1, adm jr., 7/01
|
||
ON2 P3 ON2 80.0 104.3 !nad/ppi, jjp1/adm jr. 7/95
|
||
ON2 P3 ON3 88.9 111.6 !nad/ppi, jjp1/adm jr. 7/95
|
||
ON2 P4 ON3 88.9 105.0 !PPI2, from nad/ppi, adm jr., 7/01
|
||
ON3 P3 ON3 104.0 120.0 !nad/ppi, jjp1/adm jr. 7/95
|
||
ON3 P4 ON3 104.0 120.0 !PPI2, from nad/ppi, adm jr., 7/01
|
||
|
||
DIHEDRALS
|
||
!
|
||
!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
|
||
!
|
||
!Kchi: kcal/mole
|
||
!n: multiplicity
|
||
!delta: degrees
|
||
!
|
||
!atom types Kchi n delta
|
||
!2-(aminobutyl)-1,3-propandiol terms
|
||
X CN8 ON2 X -0.10 3 0.0 ! phosphate ester
|
||
X CN7 CN8 X 0.20 3 0.0 ! alkane
|
||
X CN8 NN6 X 0.10 3 0.0 ! methylammonium
|
||
!abasic nucleoside terms - susil
|
||
CN7 ON6 CN8B HN8 0.195 1 0.0
|
||
ON6 CN8B CN8 HN8 0.195 1 0.0
|
||
HN7 CN7 ON6 CN8B 0.195 3 0.0
|
||
CN8B CN8 CN7 HN7 0.195 3 0.0
|
||
HN8 CN8B CN8 HN8 0.195 3 0.0
|
||
HN8 CN8B CN8 CN7 0.195 3 0.0
|
||
! c5'-c4'-o4'-c1', exo
|
||
CN8B CN7 ON6 CN8B 0.5 5 0.0 ! min at 150 310 max at 25 200
|
||
CN8B CN7 ON6 CN8B 0.1 3 180.0
|
||
CN8B CN7 ON6 CN8B 0.5 1 0.0
|
||
! c1'-c2'-c3'-o3', exo
|
||
CN8B CN8 CN7 ON5 0.4 5 0.0
|
||
CN8B CN8 CN7 ON5 0.4 3 0.0
|
||
CN8B CN8 CN7 ON5 0.7 2 0.0 !elevates energy at 0 (c3'endo), adm
|
||
CN8B CN8 CN7 ON5 0.5 1 180.0 !elevates energy at 0 (c3'endo), adm
|
||
CN8B CN8 CN7 ON2 0.4 5 0.0 !terms for oligonuclotide
|
||
CN8B CN8 CN7 ON2 0.4 3 0.0
|
||
CN8B CN8 CN7 ON2 0.7 2 0.0
|
||
CN8B CN8 CN7 ON2 0.5 1 180.0
|
||
! c4'-o4'-c1'-c2', tau0
|
||
CN7 ON6 CN8B CN8 0.6 6 180.0
|
||
CN7 ON6 CN8B CN8 0.6 3 0.0
|
||
! o4'-c1'-c2'-c3', tau1
|
||
ON6 CN8B CN8 CN7 0.7 5 180.0 !lowers 90, shifts c2endo minimum towards 200
|
||
ON6 CN8B CN8 CN7 0.4 4 0.0 !lowers 90, shifts c2endo minimum towards 200
|
||
ON6 CN8B CN8 CN7 0.4 3 180.0 !lowers 90, shifts c2endo minimum towards 200
|
||
! c4'-c3'-c2'-c1', tau2
|
||
CN7 CN7 CN8 CN8B 0.5 4 0.0
|
||
CN7 CN7 CN8 CN8B 0.1 3 0.0 !lowers energy in 150 to 250 range
|
||
! c1'-o4'-c4'-c3', tau4
|
||
CN8B ON6 CN7 CN7 0.5 3 0.0 !effects surface in 200-360 region
|
||
|
||
! PHOSPHATE
|
||
ON2 P2 ON2 CN7 0.90 1 180.0 ! adm, 2011 DNA update new param, zeta, kat2 set
|
||
ON2 P2 ON2 CN7 0.40 2 180.0 ! adm, 2011 DNA update new param, zeta, kat2 set
|
||
ON2 P2 ON2 CN7 0.20 3 180.0 ! adm, 2011 DNA update new param, zeta, kat2 set
|
||
ON2 P ON2 CN7 1.20 1 180.0 !10/97, DMP, adm jr., RNA
|
||
ON2 P ON2 CN7 0.10 2 180.0 !10/97, DMP, adm jr., RNA
|
||
ON2 P ON2 CN7 0.10 3 180.0 !10/97, DMP, adm jr., RNA
|
||
ON2 P ON2 CN7 0.00 6 0.0 !10/97, DMP, adm jr., RNA
|
||
ON2 P ON2 CN8 1.20 1 180.0 !10/97, DMP, adm jr.
|
||
ON2 P ON2 CN8 0.10 2 180.0 !10/97, DMP, adm jr.
|
||
ON2 P ON2 CN8 0.10 3 180.0 !10/97, DMP, adm jr.
|
||
ON2 P ON2 CN8 0.00 6 0.0 !10/97, DMP, adm jr.
|
||
ON2 P2 ON2 CN8 1.20 1 180.0 !10/97, DMP, adm jr., adm 2011 DNA update
|
||
ON2 P2 ON2 CN8 0.10 2 180.0 !10/97, DMP, adm jr., adm 2011 DNA update
|
||
ON2 P2 ON2 CN8 0.10 3 180.0 !10/97, DMP, adm jr., adm 2011 DNA update
|
||
ON2 P2 ON2 CN8 0.00 6 0.0 !10/97, DMP, adm jr., adm 2011 DNA update
|
||
! Added when C5' defined as CN8B (NF 041497):
|
||
ON2 P2 ON2 CN8B 1.20 1 180.0 !10/97, DMP, adm jr., adm, 2011 DNA update
|
||
ON2 P2 ON2 CN8B 0.10 2 180.0 !10/97, DMP, adm jr., adm, 2011 DNA update
|
||
ON2 P2 ON2 CN8B 0.10 3 180.0 !10/97, DMP, adm jr., adm, 2011 DNA update
|
||
ON2 P2 ON2 CN8B 0.00 6 0.0 !10/97, DMP, adm jr., adm, 2011 DNA update
|
||
ON2 P ON2 CN8B 1.20 1 180.0 !10/97, DMP, adm jr., RNA
|
||
ON2 P ON2 CN8B 0.10 2 180.0 !10/97, DMP, adm jr., RNA
|
||
ON2 P ON2 CN8B 0.10 3 180.0 !10/97, DMP, adm jr., RNA
|
||
ON2 P ON2 CN8B 0.00 6 0.0 !10/97, DMP, adm jr., RNA
|
||
ON2 P ON2 CN9 1.20 1 180.0 !dmp
|
||
ON2 P ON2 CN9 0.10 2 180.0 !dmp
|
||
ON2 P ON2 CN9 0.10 3 180.0 !dmp
|
||
ON2 P ON2 CN9 0.00 6 0.0 !dmp
|
||
ON2 P2 ON2 CN9 1.20 1 180.0 !dmp, adm, 2011 DNA update
|
||
ON2 P2 ON2 CN9 0.10 2 180.0 !dmp, adm, 2011 DNA update
|
||
ON2 P2 ON2 CN9 0.10 3 180.0 !dmp, adm, 2011 DNA update
|
||
ON2 P2 ON2 CN9 0.00 6 0.0 !dmp, adm, 2011 DNA update
|
||
!
|
||
ON3 P ON2 CN7 0.10 3 0.0 !dmp,eps, O1P-P-O3'-C3'
|
||
ON3 P2 ON2 CN7 0.10 3 0.0 !dmp,eps, O1P-P-O3'-C3', adm, 2011 DNA update
|
||
ON3 P ON2 CN7B 0.10 3 0.0 !for NADPH and bkbmod
|
||
ON3 P ON2 CN8 0.10 3 0.0 !dmp
|
||
ON3 P2 ON2 CN8 0.10 3 0.0 !dmp, adm 2011 DNA update
|
||
ON3 P ON2 CN8B 0.10 3 0.0 !dmp,bet, O1P-P-O5'-C5'
|
||
ON3 P2 ON2 CN8B 0.10 3 0.0 !dmp,bet, O1P-P-O5'-C5', adm, 2011 DNA update
|
||
ON3 P ON2 CN9 0.10 3 0.0 !dmp
|
||
ON3 P2 ON2 CN9 0.10 3 0.0 !dmp, adm, 2011 DNA update
|
||
! terminal phosphate terms, adm jr.
|
||
ON4 P ON2 CN7 0.95 2 0.0 !MP_1, adm jr.
|
||
ON4 P ON2 CN7 0.50 3 0.0 !MP_1, adm jr.
|
||
ON4 P2 ON2 CN7 0.95 2 0.0 !MP_1, adm jr., adm, 2011 DNA update
|
||
ON4 P2 ON2 CN7 0.50 3 0.0 !MP_1, adm jr., adm, 2011 DNA update
|
||
ON4 P ON2 CN8 0.95 2 0.0 !MP_1, adm jr.
|
||
ON4 P ON2 CN8 0.50 3 0.0 !MP_1, adm jr.
|
||
ON4 P ON2 CN8B 0.95 2 0.0 !MP_1, adm jr.
|
||
ON4 P ON2 CN8B 0.50 3 0.0 !MP_1, adm jr.
|
||
ON4 P2 ON2 CN8B 0.95 2 0.0 !MP_1, adm jr., adm, 2011 DNA update
|
||
ON4 P2 ON2 CN8B 0.50 3 0.0 !MP_1, adm jr., adm, 2011 DNA update
|
||
ON4 P ON2 CN9 0.95 2 0.0 !MP_1, adm jr.
|
||
ON4 P ON2 CN9 0.50 3 0.0 !MP_1, adm jr.
|
||
ON4 P2 ON2 CN9 0.95 2 0.0 !MP_1, adm jr., adm, 2011 DNA update
|
||
ON4 P2 ON2 CN9 0.50 3 0.0 !MP_1, adm jr., adm, 2011 DNA update
|
||
X ON4 P X 0.30 3 0.0 !MP_1, adm jr.
|
||
X ON4 P2 X 0.30 3 0.0 !MP_1, adm jr., adm, 2011 DNA update
|
||
! When O5' is ON2 (phosphodiester linkage):
|
||
P ON2 CN7 HN7 0.000 3 0.0 !dmp,eps, H-C3'-O3'-P
|
||
P2 ON2 CN7 HN7 0.000 3 0.0 !dmp,eps, H-C3'-O3'-P, adm, 2011 DNA update
|
||
P ON2 CN7B HN7 0.000 3 0.0 !for NADPH and bkbmod
|
||
P ON2 CN8B HN8 0.000 3 0.0 !dmp,beta, H-C5'-O5'-P
|
||
P2 ON2 CN8B HN8 0.000 3 0.0 !dmp,beta, H-C5'-O5'-P, adm, 2011 DNA update
|
||
P ON2 CN8 HN8 0.000 3 0.0 !dmp
|
||
P ON2 CN9 HN9 0.000 3 0.0 !dmp
|
||
P2 ON2 CN9 HN9 0.000 3 0.0 !dmp, adm, 2011 DNA update
|
||
! butane gauche terms
|
||
cn9 cn8 cn8 cn9 0.15 1 0.0
|
||
cn9 cn8 cn8 cn8 0.15 1 0.0
|
||
! BASES
|
||
! Uracil
|
||
NN2B CN1T NN2U CN1 1.5 2 180.0 ! adm jr. 11/97
|
||
CN1T NN2U CN1 CN3 1.5 2 180.0 ! adm jr. 11/97
|
||
NN2U CN1 CN3 CN3 1.5 2 180.0 ! adm jr. 11/97
|
||
CN1 CN3 CN3 NN2B 6.0 2 180.0 ! adm jr. 11/97
|
||
CN3 CN3 NN2B CN1T 1.5 2 180.0 ! adm jr. 11/97
|
||
CN3 NN2B CN1T NN2U 1.5 2 180.0 ! adm jr. 11/97
|
||
HN3 CN3 CN3 HN3 3.0 2 180.0 ! adm jr. 11/97
|
||
HN3 CN3 CN1 ON1 6.0 2 180.0 ! adm jr. 11/97
|
||
ON1 CN1T NN2B HN2 0.0 2 180.0 ! adm jr. 11/97
|
||
ON1 CN1 NN2U HN2 0.0 2 180.0 ! adm jr. 11/97
|
||
ON1 CN1T NN2U HN2 0.0 2 180.0 ! adm jr. 11/97
|
||
HN2 NN2B CN3 HN3 1.5 2 180.0 ! adm jr. 11/97
|
||
NN2B CN1T NN2U HN2 3.8 2 180.0 ! adm jr. 11/97
|
||
CN3 CN1 NN2U HN2 3.8 2 180.0 ! adm jr. 11/97
|
||
CN3 CN3 NN2B HN2 1.6 2 180.0 ! adm jr. 11/97
|
||
NN2U CN1T NN2B HN2 1.6 2 180.0 ! adm jr. 11/97
|
||
!Thymine
|
||
CN1T NN2B CN3 CN3T 1.8 2 180.0 ! adm jr. 11/97
|
||
NN2U CN1 CN3T CN3 1.8 2 180.0 ! adm jr. 11/97
|
||
CN1 CN3T CN3 NN2B 3.0 2 180.0 ! adm jr. 11/97
|
||
NN2B CN1 CN3T CN9 5.6 2 180.0 ! adm jr. 11/97
|
||
NN2B CN3 CN3T CN9 5.6 2 180.0 ! adm jr. 11/97
|
||
CN1 CN3T CN9 HN9 0.46 3 0.0 ! adm jr. 11/97
|
||
CN3 CN3T CN9 HN9 0.46 3 0.0 ! adm jr. 11/97
|
||
CN3T CN1 NN2U HN2 4.8 2 180.0 ! adm jr. 11/97
|
||
! Cytosine
|
||
CN3 NN2 CN1 NN3 0.6 2 180.0 ! adm jr. 11/97
|
||
NN2 CN1 NN3 CN2 0.6 2 180.0 ! adm jr. 11/97
|
||
CN1 NN3 CN2 CN3 6.0 2 180.0 ! adm jr. 11/97
|
||
NN3 CN2 CN3 CN3 0.6 2 180.0 ! adm jr. 11/97
|
||
CN2 CN3 CN3 NN2 6.0 2 180.0 ! adm jr. 11/97
|
||
CN3 CN3 NN2 CN1 0.6 2 180.0 ! adm jr. 11/97
|
||
NN3 CN2 NN1 HN1 1.0 2 180.0 ! adm jr. 11/97
|
||
CN3 CN2 NN1 HN1 1.0 2 180.0 ! adm jr. 11/97
|
||
NN1 CN2 NN3 CN1 2.0 2 180.0 ! adm jr. 11/97
|
||
NN1 CN2 CN3 CN3 2.0 2 180.0 ! adm jr. 11/97
|
||
NN1 CN2 CN3 HN3 2.0 2 180.0 ! adm jr. 11/97
|
||
ON1C CN1 NN2 HN2 3.0 2 180.0 ! adm jr. 11/97
|
||
ON1C CN1 NN3 CN2 1.6 2 180.0 ! adm jr. 11/97
|
||
ON1C CN1 NN2 CN3 1.6 2 180.0 ! adm jr. 11/97
|
||
NN3 CN2 CN3 HN3 3.4 2 180.0 ! adm jr. 11/97
|
||
NN2 CN3 CN3 HN3 3.4 2 180.0 ! adm jr. 11/97
|
||
CN2 CN3 CN3 HN3 4.6 2 180.0 ! adm jr. 11/97
|
||
CN1 NN2 CN3 HN3 4.6 2 180.0 ! adm jr. 11/97
|
||
X CN2 NN3 X 2.0 2 180.0 ! adm jr. 11/97
|
||
! Adenine
|
||
CN2 NN3A CN4 NN3A 1.8 2 180.0 ! adm jr. 11/97, 6-mem
|
||
NN3A CN4 NN3A CN5 2.0 2 180.0 !
|
||
CN4 NN3A CN5 CN5 1.8 2 180.0 !
|
||
NN3A CN5 CN5 CN2 2.0 2 180.0 ! treated 2x
|
||
CN5 CN5 CN2 NN3A 1.8 2 180.0 !
|
||
CN5 CN2 NN3A CN4 10.0 2 180.0 !
|
||
CN5 CN5 NN4 CN4 6.0 2 180.0 ! 5-mem
|
||
CN5 NN4 CN4 NN2 14.0 2 180.0 !
|
||
NN4 CN4 NN2 CN5 6.0 2 180.0 !
|
||
CN4 NN2 CN5 CN5 6.0 2 180.0 !
|
||
NN2 CN5 CN5 NN4 14.0 2 180.0 ! treated 2x
|
||
CN2 NN3A CN4 HN3 8.5 2 180.0 ! H2
|
||
CN5 NN3A CN4 HN3 8.5 2 180.0 ! H2
|
||
CN5 NN4 CN4 HN3 5.2 2 180.0 ! H8
|
||
CN5 NN2 CN4 HN3 5.2 2 180.0 ! H8
|
||
CN5 CN5 NN2 HN2 1.2 2 180.0 ! H9
|
||
NN4 CN4 NN2 HN2 1.2 2 180.0 ! H9
|
||
HN2 NN2 CN4 HN3 0.0 2 180.0 ! H8-C-N-H9
|
||
CN4 NN3A CN2 NN1 4.0 2 180.0 ! N6
|
||
CN5 CN5 CN2 NN1 4.0 2 180.0 ! N6
|
||
NN4 CN5 CN2 NN1 0.0 2 180.0 ! N6
|
||
CN5 CN2 NN1 HN1 0.5 2 180.0 ! 6-NH2
|
||
NN3A CN2 NN1 HN1 0.5 2 180.0 !
|
||
! Butterfly motion
|
||
NN3A CN5 CN5 NN4 7.0 2 180.0 !A, adm jr. 11/97
|
||
CN2 CN5 CN5 NN2 7.0 2 180.0 !A
|
||
NN3A CN2 CN5 NN4 2.0 2 180.0 !A
|
||
CN2 CN5 NN4 CN4 2.0 2 180.0 !A
|
||
CN4 NN3A CN5 NN2 2.0 2 180.0 !A
|
||
NN3A CN5 NN2 CN4 2.0 2 180.0 !A
|
||
! Guanine
|
||
CN1 NN2G CN2 NN3G 0.2 2 180.0 !adm jr. 11/97, 6-mem
|
||
NN2G CN2 NN3G CN5 2.0 2 180.0 !
|
||
CN2 NN3G CN5 CN5G 0.2 2 180.0 !
|
||
NN3G CN5 CN5G CN1 2.0 2 180.0 !
|
||
CN5 CN5G CN1 NN2G 0.2 2 180.0 !
|
||
CN5G CN1 NN2G CN2 0.2 2 180.0 !
|
||
CN5 CN5G NN4 CN4 6.0 2 180.0 !5-mem
|
||
CN5G NN4 CN4 NN2B 16.0 2 180.0 !
|
||
NN4 CN4 NN2B CN5 6.0 2 180.0 !
|
||
CN4 NN2B CN5 CN5G 6.0 2 180.0 !
|
||
NN2B CN5 CN5G NN4 10.0 2 180.0 !
|
||
! substitutents
|
||
ON1 CN1 CN5G CN5 14.0 2 180.0 !G, O6
|
||
ON1 CN1 CN5G NN4 0.0 2 180.0 !
|
||
ON1 CN1 NN2G CN2 14.0 2 180.0 !
|
||
ON1 CN1 NN2G HN2 0.0 2 180.0 !
|
||
NN1 CN2 NN2G CN1 4.0 2 180.0 !G, N2
|
||
NN1 CN2 NN3G CN5 4.0 2 180.0 !
|
||
NN1 CN2 NN2G HN2 0.0 2 180.0 !
|
||
NN2G CN2 NN1 HN1 1.2 2 180.0 !
|
||
NN3G CN2 NN1 HN1 1.2 2 180.0 !
|
||
HN2 NN2G CN1 CN5G 3.6 2 180.0 !G, H1
|
||
HN2 NN2G CN2 NN3G 3.6 2 180.0 !
|
||
HN3 CN4 NN4 CN5G 5.6 2 180.0 !G, H8
|
||
HN3 CN4 NN2B CN5 5.6 2 180.0 !
|
||
HN3 CN4 NN2B HN2 0.0 2 180.0 !
|
||
HN2 NN2B CN5 CN5G 1.2 2 180.0 !G, H9
|
||
HN2 NN2B CN5 NN3G 1.2 2 180.0 !
|
||
HN2 NN2B CN4 NN4 1.2 2 180.0 !
|
||
! Butterfly motion
|
||
NN3G CN5 CN5G NN4 10.0 2 180.0 !adm jr. 11/97
|
||
CN1 CN5G CN5 NN2 10.0 2 180.0 !
|
||
NN2G CN1 CN5G NN4 2.0 2 180.0 !
|
||
CN1 CN5G NN4 CN4 2.0 2 180.0 !
|
||
CN2 NN3G CN5 NN2B 2.0 2 180.0 !
|
||
NN3G CN5 NN2B CN4 2.0 2 180.0 !
|
||
! Wild cards for uracil, thymine and cytosine
|
||
X CN1 NN3 X 1.0 2 180.0 ! c22
|
||
X CN1 NN2 X 0.9 2 180.0 ! c22
|
||
X CN1T NN2B X 0.9 2 180.0 ! From X CN1 NN2 X, for thymines
|
||
X CN1 NN2G X 0.9 2 180.0 ! c22
|
||
X CN1 NN2U X 0.9 2 180.0 ! c22
|
||
X CN1T NN2U X 0.9 2 180.0 ! c22
|
||
X CN3 NN2 X 1.0 2 180.0 ! c22
|
||
X CN3 NN2B X 1.0 2 180.0 ! From X CN3 NN2 X, for thymines
|
||
X CN3 CN3 X 1.0 2 180.0 ! c22
|
||
X CN3 CN3T X 1.0 2 180.0 !T, adm jr. 11/97
|
||
X CN1 CN3 X 1.0 2 180.0 ! c22
|
||
X CN1 CN3T X 1.0 2 180.0 !T, adm jr. 11/97
|
||
X CN2 CN3 X 0.8 2 180.0 ! c22
|
||
! Wild cards for adenine and guanine
|
||
X CN1 CN5G X 1.0 2 180.0 ! adm jr. 11/97
|
||
X CN2 NN2G X 1.0 2 180.0 !
|
||
X CN2 CN5 X 1.0 2 180.0 !
|
||
X CN4 NN2 X 1.5 2 180.0 !
|
||
X CN4 NN2B X 1.5 2 180.0 ! From X CN4 NN2 X
|
||
X CN4 NN3A X 3.5 2 180.0 !
|
||
X CN4 NN4 X 2.0 2 180.0 ! A,G
|
||
X CN5 CN5 X 0.0 2 180.0 !
|
||
X CN5G CN5 X 0.0 2 180.0 ! adm jr. 11/97
|
||
X CN5 NN2 X 1.5 2 180.0 !
|
||
X CN5 NN2B X 1.5 2 180.0 ! From X CN5 NN2 X
|
||
X CN5 NN3A X 1.0 2 180.0 !
|
||
X CN5 NN3G X 1.0 2 180.0 ! adm jr. 11/97
|
||
X CN5 NN4 X 1.0 2 180.0 !
|
||
X CN5G NN4 X 1.0 2 180.0 ! adm jr. 11/97
|
||
X CN2 NN3A X 1.0 2 180.0 !
|
||
X CN2 NN3G X 1.0 2 180.0 ! adm jr. 11/97
|
||
! MISC.
|
||
CN1 NN2 CN9 HN9 0.19 3 0.0 ! 1-M-C
|
||
CN3 NN2 CN9 HN9 0.00 3 0.0 ! 1-M-C
|
||
CN4 NN2 CN9 HN9 0.00 3 0.0 ! 9-M-A
|
||
CN5 NN2 CN9 HN9 0.19 3 0.0 ! 9-M-A
|
||
CN1 NN2B CN9 HN9 0.19 3 0.0 ! 1-M-U
|
||
CN1T NN2B CN9 HN9 0.19 3 0.0 ! 1-M-T
|
||
CN3 NN2B CN9 HN9 0.00 3 0.0 ! 1-M-T/U
|
||
CN4 NN2B CN9 HN9 0.00 3 0.0 ! 9-M-G
|
||
CN5 NN2B CN9 HN9 0.19 3 0.0 ! 9-M-G
|
||
CN4 NN2B CN8 HN8 0.00 3 0.0 ! 9-E-G
|
||
CN5 NN2B CN8 HN8 0.19 3 0.0 ! 9-E-G
|
||
CN4 NN2B CN8 CN9 0.00 3 0.0 ! 9-E-G
|
||
CN5 NN2B CN8 CN9 0.19 3 0.0 ! 9-E-G
|
||
X CN8 CN8 X 0.15 3 0.0 ! Alkanes (0.2 to 0.15)
|
||
X CN8 CN9 X 0.15 3 0.0 ! Alkanes (0.2 to 0.15)
|
||
!for nadp/nadph, adm jr.
|
||
HN7 CN7B CN7B ON2 0.195 3 0.0 !for NADPH and bkbmod
|
||
ON2 CN7B CN7B NN2 0.0 3 0.0 !for NADPH and bkbmod
|
||
|
||
! sugar, replace with ribose terms 021998
|
||
CN7 CN7B ON6 CN7 0.6 6 180.0
|
||
CN7B CN7 CN7 CN7 0.4 6 0.0 ! good for amplitudes
|
||
CN7B CN7 CN7 CN9 0.4 6 0.0 ! good for amplitudes, 5MET
|
||
CN7 CN7 CN7 ON6 0.6 6 0.0
|
||
CN7 CN7 CN7B ON6 0.6 6 0.0
|
||
ON2 CN7 CN7 CN7 0.8 6 0.0 !
|
||
ON2 CN7 CN7 CN7 0.4 5 0.0 ! Moves the barrier right
|
||
ON2 CN7 CN7 CN7 2.0 3 180.0 !
|
||
! for ndph
|
||
ON2 CN7B CN7 CN7 0.8 6 0.0 !
|
||
ON2 CN7B CN7 CN7 0.4 5 0.0 ! Moves the barrier right
|
||
ON2 CN7B CN7 CN7 2.0 3 180.0 !
|
||
!
|
||
ON5 CN7 CN7 CN7 0.8 6 0.0 !
|
||
ON5 CN7 CN7 CN7 0.4 5 0.0 ! Moves the barrier right
|
||
ON5 CN7 CN7 CN7 2.0 3 180.0 !
|
||
ON5 CN7 CN7 ON5 0.0 3 0.0 !
|
||
ON5 CN7 CN7 ON2 0.0 3 0.0 !
|
||
ON2 CN7 CN7B ON6 0.5 6 0.0 !good for amplitudes
|
||
ON2 CN7 CN7B ON6 0.3 5 0.0 !impact on amplitudes
|
||
ON2 CN7 CN7B ON6 0.6 4 180.0 !increases c2'endo
|
||
ON2 CN7 CN7B ON6 0.2 3 0.0 !
|
||
CN7 CN7 CN7 CN8B 0.5 4 180.0 !del lowers 180 deg.
|
||
|
||
!%%%%%%% new terms for dna and the deoxyribose-based model compounds %%%%%%
|
||
! The following is for: THF3P (model for espilon), THFM3P (model for puckering),
|
||
! THF5P (model for gamma and beta), THFCH3IM (model for chi), nucleotide analogue
|
||
!@@@@@@ Begining of chi
|
||
!============= added for torsion about chi in adenine ============
|
||
!For link from sugar to base:
|
||
CN7B NN2 CN4 HN3 0.3 2 180.0 ! NF
|
||
CN7B NN2 CN5 CN5 11.0 2 180.0 ! adm jr.
|
||
CN7B NN2 CN4 NN4 11.0 2 180.0 ! adm jr.
|
||
CN7B NN2 CN4 NN3A 11.0 2 180.0 ! adm jr.
|
||
!For chi itself:
|
||
!DNA:
|
||
ON6 CN7B NN2 CN5 1.1 1 180.0 !
|
||
ON6 CN7B NN2 CN4 1.1 1 0.0 ! NF
|
||
!RNA:
|
||
ON6B CN7B NN2 CN5 1.1 1 180.0 !
|
||
ON6B CN7B NN2 CN4 1.1 1 0.0 !
|
||
!DNA:
|
||
CN8 CN7B NN2 CN5 0.3 3 0.0 ! NF
|
||
CN8 CN7B NN2 CN4 0.0 3 180.0 ! NF
|
||
!RNA:
|
||
CN7B CN7B NN2 CN5 0.3 3 0.0 ! NF
|
||
CN7B CN7B NN2 CN4 0.0 3 180.0 ! NF
|
||
|
||
HN7 CN7B NN2 CN5 0.0 3 0.0 ! NF
|
||
HN7 CN7B NN2 CN4 0.195 3 0.0 ! NF
|
||
!@@@@@@ End of chi in adenines
|
||
|
||
!============== terms for torsion about chi in cytosines ===========
|
||
CN7B NN2 CN3 HN3 0.3 2 180.0 ! NF
|
||
CN7B NN2 CN1 ON1C 11.0 2 180.0 ! adm jr. from A
|
||
CN7B NN2 CN1 NN3 11.0 2 180.0 ! adm jr.
|
||
CN7B NN2 CN3 CN3 11.0 2 180.0 ! adm jr.
|
||
!DNA:
|
||
ON6 CN7B NN2 CN1 0.0 3 0.0 !
|
||
ON6 CN7B NN2 CN3 1.0 1 0.0 ! NF
|
||
!RNA:
|
||
ON6B CN7B NN2 CN1 0.0 3 0.0 !
|
||
ON6B CN7B NN2 CN3 1.0 1 0.0 !
|
||
!DNA:
|
||
CN8 CN7B NN2 CN1 1.0 3 0.0 !
|
||
CN8 CN7B NN2 CN3 0.0 3 180.0 ! NF 030697
|
||
!RNA:
|
||
CN7B CN7B NN2 CN1 1.0 3 0.0 !
|
||
CN7B CN7B NN2 CN3 0.0 3 180.0 !
|
||
|
||
HN7 CN7B NN2 CN1 0.0 3 0.0 ! NF
|
||
HN7 CN7B NN2 CN3 0.195 3 0.0 ! NF
|
||
!@@@@@@ End of chi in cytosines
|
||
|
||
!=========== terms for torsion about chi in uracils/thymines ===========
|
||
CN7B NN2B CN3 HN3 0.3 2 180.0 ! NF
|
||
CN7B NN2B CN1T ON1 11.0 2 180.0 ! adm jr. from A
|
||
CN7B NN2B CN1T NN2U 11.0 2 180.0 ! adm jr.
|
||
CN7B NN2B CN3 CN3T 11.0 2 180.0 ! adm jr.
|
||
!DNA:
|
||
ON6 CN7B NN2B CN1 0.0 3 0.0 !
|
||
ON6 CN7B NN2B CN1T 0.7 3 0.0 !
|
||
ON6 CN7B NN2B CN1T 0.8 1 180.0 !
|
||
ON6 CN7B NN2B CN3 0.9 1 0.0 ! NF
|
||
!RNA:
|
||
ON6B CN7B NN2B CN1 0.0 3 0.0 !
|
||
ON6B CN7B NN2B CN1T 0.7 3 0.0 !
|
||
ON6B CN7B NN2B CN1T 0.8 1 180.0 !
|
||
ON6B CN7B NN2B CN3 0.9 1 0.0 !
|
||
!DNA:
|
||
CN8 CN7B NN2B CN1T 0.2 3 180.0 !
|
||
CN8 CN7B NN2B CN3 0.0 3 180.0 ! NF
|
||
!RNA:
|
||
CN7B CN7B NN2B CN1T 0.2 3 180.0 !
|
||
CN7B CN7B NN2B CN3 0.0 3 180.0 !
|
||
|
||
HN7 CN7B NN2B CN1T 0.0 3 0.0 ! NF
|
||
HN7 CN7B NN2B CN3 0.195 3 0.0 ! NF
|
||
!@@@@@@ End of chi in thymines
|
||
|
||
!============= added for torsion about chi in guanine ============
|
||
CN7B NN2B CN4 HN3 0.3 2 180.0 ! NF
|
||
CN7B NN2B CN4 NN4 11.0 2 180.0 ! adm jr.
|
||
CN7B NN2B CN5 CN5G 11.0 2 180.0 ! adm jr. from U
|
||
CN7B NN2B CN5 NN3G 11.0 2 180.0 ! adm jr.
|
||
!DNA:
|
||
ON6 CN7B NN2B CN5 0.2 3 0.0 !
|
||
ON6 CN7B NN2B CN5 1.1 1 180.0 !
|
||
ON6 CN7B NN2B CN4 1.4 1 0.0 ! NF
|
||
!RNA:
|
||
ON6B CN7B NN2B CN5 0.2 3 0.0 !
|
||
ON6B CN7B NN2B CN5 1.1 1 180.0 !
|
||
ON6B CN7B NN2B CN4 1.4 1 0.0 !
|
||
!DNA:
|
||
CN8 CN7B NN2B CN5 0.0 3 0.0 ! NF
|
||
CN8 CN7B NN2B CN4 0.0 3 180.0 ! NF 030697
|
||
!RNA:
|
||
CN7B CN7B NN2B CN5 0.0 3 0.0 ! NF
|
||
CN7B CN7B NN2B CN4 0.0 3 180.0 !
|
||
|
||
HN7 CN7B NN2B CN5 0.0 3 0.0 ! NF
|
||
HN7 CN7B NN2B CN4 0.195 3 0.0 ! NF
|
||
!@@@@@@ End of chi in guanines
|
||
!@@@@@@ link (not chi) between base and sugar for both purines and pyrimidines:
|
||
!DNA:
|
||
CN7 ON6 CN7B NN2 0.0 3 0.0
|
||
CN7 ON6 CN7B NN2B 0.0 3 0.0
|
||
!RNA:
|
||
CN7 ON6B CN7B NN2 0.0 3 0.0
|
||
CN7 ON6B CN7B NN2B 0.0 3 0.0
|
||
!DNA:
|
||
CN7 CN8 CN7B NN2 0.0 3 0.0
|
||
CN7 CN8 CN7B NN2B 0.0 3 0.0
|
||
HN8 CN8 CN7B NN2 0.0 3 0.0
|
||
HN8 CN8 CN7B NN2B 0.0 3 0.0
|
||
!RNA:
|
||
CN7 CN7B CN7B NN2 0.0 3 0.0
|
||
CN7 CN7B CN7B NN2B 0.0 3 0.0
|
||
!RNA
|
||
HN7 CN7B CN7B NN2 0.0 3 0.0
|
||
HN7 CN7B CN7B NN2B 0.0 3 0.0
|
||
|
||
!@@@@@@ Begining of torsions involving exocyclic sugar atoms:
|
||
!======= CN7 CN8B ON2 P = C4'-C5'-O5'-P
|
||
CN7 CN8B ON2 P 0.2 1 120.0 !bet C4'-C5'-O5'-P, adm jr.
|
||
CN7 CN8B ON2 P2 0.2 1 120.0 !bet C4'-C5'-O5'-P, adm jr., adm, 2011 DNA update
|
||
! the following differ significantly from the alcohols
|
||
! in the protein (based on ethanol), they also differ from other
|
||
! NA C-C-OH-H parameters (see below)
|
||
! The two following terms have been replaced by their ethanol
|
||
! counterpart (NF, 083098)
|
||
CN7 CN8B ON5 HN5 1.3300 1 0.00
|
||
CN7 CN8B ON5 HN5 0.1800 2 0.00
|
||
CN7 CN8B ON5 HN5 0.3200 3 0.00
|
||
!======= HN8 CN8B ON2 P = H-C5'-O5'-P )beta
|
||
HN8 CN8B ON5 HN5 0.0 3 0.0 !bet
|
||
!======== CN7 CN7 CN8B ON2 = C3'-C4'-C5'-O5'
|
||
! When O5' is ON2 (phosphodiester linkage):
|
||
CN7 CN7 CN8B ON2 0.20 4 180.0 !gam adm jr.
|
||
CN7 CN7 CN8B ON2 0.80 3 180.0 !gam C3'-C4'-C5'-O5'
|
||
CN7 CN7 CN8B ON2 0.40 2 0.0 !gam
|
||
CN7 CN7 CN8B ON2 2.50 1 180.0 !gam
|
||
!
|
||
CN8 CN7 CN8B ON2 0.2 3 180.0 ! from gam, carbocyclic and 25P1
|
||
! When O5' is ON5 (5TER patch):
|
||
CN7 CN7 CN8B ON5 0.20 4 180.0 !gam adm jr.
|
||
CN7 CN7 CN8B ON5 0.80 3 180.0 !gam C3'-C4'-C5'-O5'
|
||
CN7 CN7 CN8B ON5 0.40 2 0.0 !gam
|
||
CN7 CN7 CN8B ON5 2.50 1 180.0 !gam
|
||
!======== ON6 CN7 CN8B ON2 = O4'-C4'-C5'-O5'
|
||
! When O5' is ON2 (3'-5' phosphodiester linkage)
|
||
ON6 CN7 CN8B ON2 3.4 1 180.0 !gam O4'-C4'-C5'-O5',influences +60
|
||
ON6B CN7 CN8B ON2 3.4 1 180.0 !gam, RNA
|
||
! When O5' is ON5 (5TER patch):
|
||
ON6 CN7 CN8B ON5 3.4 1 180.0 !gam
|
||
ON6B CN7 CN8B ON5 3.4 1 180.0 !gam, RNA
|
||
!======== HN8 CN8B CN7 CN7 = H-C5'-C4'-H
|
||
HN8 CN8B CN7 CN7 0.195 3 0.0 !gam,H-C5'-C4'-H
|
||
HN8 CN8B CN7 CN8 0.195 1 0.0 !gam, carbocylic, 25P1
|
||
!======== HN7 CN8B CN7 ON6 = H-C5'-C4'-O4'
|
||
HN8 CN8B CN7 ON6 0.195 1 0.0 !gam,H-C5'-C4'-O4'
|
||
HN8 CN8B CN7 ON6B 0.195 1 0.0 !gam, RNA
|
||
!======== HN7 CN7 CN8B ON2 = H-C4'-C5'-O5'
|
||
! When O5' is ON2 (phosphodiester linkage):
|
||
HN7 CN7 CN8B ON2 0.195 3 0.0 !gam H-C4'-C5'-O5'
|
||
! When O5' is ON5 (5TER patch):
|
||
HN7 CN7 CN8B ON5 0.195 3 0.0 !gam
|
||
HN8 CN8 CN8 ON6 0.195 1 0.0 !gam,H-C5'-C4'-O4'
|
||
! terms for 5MET patch
|
||
CN9 CN7 CN7 CN8B 0.5 4 180.0 !cn8 -> cn9
|
||
HN7 CN7 CN9 HN9 0.195 3 0.0 !cn8 -> cn9
|
||
CN7 CN7 CN9 HN9 0.195 3 0.0 !cn8 -> cn9
|
||
ON6 CN7 CN9 HN9 0.195 3 0.0 !cn7 -> cn9
|
||
HN7 CN7 CN7 CN9 0.195 3 0.0 !cn8 -> cn9
|
||
ON2 CN7 CN7 CN9 0.2 4 0.0 !cn8b -> cn9
|
||
ON2 CN7 CN7 CN9 0.8 3 180.0 !cn8b -> cn9
|
||
CN8 CN7 CN7 CN9 0.5 4 180.0 !cn8b -> cn9
|
||
|
||
!======== CN8 CN7 CN7 CN8B = C2'-C3'-C4'-C5'
|
||
! This term is well suited to modify the puckering surfaces, in
|
||
! particular because it is present in THF5P
|
||
CN8 CN7 CN7 CN8B 0.5 4 180.0 !del lowers 180 deg.
|
||
CN7B CN7 CN7 CN8B 0.2 4 180.0 !del, RNA
|
||
!======== CN8B CN7 CN7 ON2 = C5'-C4'-C3'-O3'
|
||
! These terms affect the c2endo/c3endo energy difference
|
||
! When O3' is ON2 (3'-5' phosphodiester linkage)
|
||
ON2 CN7 CN7 CN8B 0.2 4 0.0 !del
|
||
! the following term controls the location of the barrier at ~75 deg.
|
||
ON2 CN7 CN7 CN8B 0.8 3 180.0 !del,decreases P [100,250]
|
||
! When O3' is ON5 (patch 3TER)
|
||
ON5 CN7 CN7 CN8B 0.2 4 0.0 !
|
||
ON5 CN7 CN7 CN8B 0.8 3 180.0 !
|
||
!======== ON6 CN7 CN7 ON2 = O4'-C4'-C3'-O3'
|
||
! These terms contribute to delta
|
||
! These terms are present in THF3P and THFM3P but not in THF5P
|
||
! When O3' is ON2 (3'-5' phosphodiester linkage)
|
||
ON2 CN7 CN7 ON6 0.5 6 0.0 !del, good for amplitudes
|
||
ON2 CN7 CN7 ON6 0.3 5 0.0 !del, impact on amplitudes
|
||
ON2 CN7 CN7 ON6 0.6 4 180.0 !del, increases c2'endo
|
||
ON2 CN7 CN7 ON6 0.2 3 0.0 !
|
||
ON2 CN7 CN7 ON6B 0.4 6 0.0 !del, RNA, good for amplitudes
|
||
ON2 CN7 CN7 ON6B 0.0 5 0.0 !del, RNA, impact on amplitudes
|
||
ON2 CN7 CN7 ON6B 0.0 4 180.0 !del, RNA, increases c2'endo
|
||
ON2 CN7 CN7 ON6B 1.6 3 0.0 !del, RNA, increases C2'endo
|
||
! for ndph: make identical to ON2 CN7 CN7 ON6B
|
||
ON2 CN7B CN7B ON6B 0.4 6 0.0 !del, RNA, good for amplitudes
|
||
ON2 CN7B CN7B ON6B 0.0 5 0.0 !del, RNA, impact on amplitudes
|
||
ON2 CN7B CN7B ON6B 0.0 4 180.0 !del, RNA, increases c2'endo
|
||
ON2 CN7B CN7B ON6B 1.6 3 0.0 !del, RNA, increases C2'endo
|
||
! When O3' is ON5 (patch 3TER)
|
||
ON5 CN7 CN7 ON6 0.5 6 0.0 !
|
||
ON5 CN7 CN7 ON6 0.3 5 0.0 !
|
||
ON5 CN7 CN7 ON6 0.6 4 180.0 !
|
||
ON5 CN7 CN7 ON6 0.2 3 0.0 !
|
||
ON5 CN7 CN7 ON6B 0.4 6 0.0 !RNA
|
||
ON5 CN7 CN7 ON6B 0.0 5 0.0 !RNA
|
||
ON5 CN7 CN7 ON6B 0.0 4 180.0 !RNA
|
||
ON5 CN7 CN7 ON6B 1.6 3 0.0 !RNA. increases c2'endo
|
||
|
||
!======== CN8B CN7 ON6 CN7B = C5'-C4'-O4'-C1'
|
||
! This term can be used to adjust the c2'endo/c3'endo
|
||
! energy difference in THF5P
|
||
CN7B ON6 CN7 CN8B 0.8 3 0.0 ! P [30,80]
|
||
CN7B ON6B CN7 CN8B 2.0 3 0.0 ! To lower barrier in RNA
|
||
CN7B ON6B CN7 CN9 2.0 3 0.0 ! To lower barrier in RNA, 5MET
|
||
!======== ON2 CN7 CN8 CN7B = O3'-C3'-C2'-C1'
|
||
! This term can be used to adjust the c2'endo/c3'endo
|
||
! When O3' is ON2
|
||
ON2 CN7 CN8 CN7B 0.8 6 0.0 !
|
||
ON2 CN7 CN8 CN7B 0.4 5 0.0 ! Moves the barrier right
|
||
ON2 CN7 CN8 CN7B 2.0 3 180.0 !
|
||
ON2 CN7 CN7B CN7B 0.6 6 0.0 ! RNA
|
||
ON2 CN7 CN7B CN7B 0.0 5 0.0 ! RNA c2/c3 endo in RNA
|
||
ON2 CN7 CN7B CN7B 1.6 3 180.0 !
|
||
!When O3' is ON5 (patch 3TER)
|
||
ON5 CN7 CN8 CN7B 0.8 6 0.0 !
|
||
ON5 CN7 CN8 CN7B 0.4 5 0.0 !
|
||
ON5 CN7 CN8 CN7B 2.0 3 180.0 !
|
||
ON5 CN7 CN7B CN7B 0.6 6 0.0 ! RNA, c2/c3 endo
|
||
ON5 CN7 CN7B CN7B 0.0 5 0.0 ! RNA
|
||
ON5 CN7 CN7B CN7B 1.6 3 180.0 ! RNA
|
||
!======== ON2 CN7 CN8 HN8 = O3'-C3'-C2'-H
|
||
ON2 CN7 CN8 HN8 0.195 3 0.0 !
|
||
ON5 CN7 CN8 HN8 0.195 3 180.0 !
|
||
ON2 CN7 CN7B HN7 0.195 3 0.0 ! RNA
|
||
ON5 CN7 CN7B HN7 0.195 3 180.0 ! RNA
|
||
!======== HN7 CN7 CN7 ON2 = H-C4'-C3'-O3'
|
||
HN7 CN7 CN7 ON2 0.195 3 0.0
|
||
HN7 CN7 CN7 ON5 0.195 3 0.0
|
||
!======== CN7 CN7 ON2 P = C4'-C3'-O3'-P
|
||
CN7 CN7 ON2 P2 0.6 5 0.0 !eps, adm, 2011 DNA update
|
||
CN7 CN7 ON2 P2 0.2 4 0.0 !eps, locat of 200 mimima, adm, 2011 DNA update
|
||
CN7 CN7 ON2 P2 0.0 3 180.0 !eps, barE beteen minima, adm, 2011 DNA update
|
||
CN7 CN7 ON2 P2 0.4 2 0.0 !eps, relE of 200 vs 275 min, adm, 2011 DNA update
|
||
CN7 CN7 ON2 P2 1.9 1 180.0 !eps, adm, 2011 DNA update
|
||
CN7 CN7 ON2 P 0.6 5 0.0 !eps, RNA
|
||
CN7 CN7 ON2 P 0.2 4 0.0 !eps, locat of 200 mimima, RNA
|
||
CN7 CN7 ON2 P 0.0 3 180.0 !eps, barE beteen minima, RNA
|
||
CN7 CN7 ON2 P 0.4 2 0.0 !eps, relE of 200 vs 275 min, RNA
|
||
CN7 CN7 ON2 P 1.9 1 180.0 !eps, RNA
|
||
!======== CN8 CN7 ON2 P = C2'-C3'-O3'-P
|
||
! This term is involved in epsilon
|
||
CN8 CN7 ON2 P 2.5 1 180.0 ! 3-terminal phosphate
|
||
CN8 CN7 ON2 P2 1.9 1 180.0 ! adm, 2011 DNA update new param, eps
|
||
CN7B CN7 ON2 P 2.5 1 180.0 !eps, RNA
|
||
CN7B CN7B ON2 P 2.5 1 180.0 !eps, NADPH and bkbmod
|
||
CN7 CN7B ON2 P 2.5 1 180.0 !eps, NADPH and bkbmod
|
||
! base on thfalloh
|
||
! the following differ significantly from the protein based
|
||
! alcohol parameters (based on ethanol, see above)
|
||
CN7 CN7 ON5 HN5 0.5 3 0.0
|
||
CN7 CN7 ON5 HN5 0.3 2 180.0
|
||
CN7 CN7 ON5 HN5 1.5 1 0.0
|
||
CN8 CN7 ON5 HN5 0.5 3 0.0
|
||
CN8 CN7 ON5 HN5 1.0 2 180.0
|
||
CN8 CN7 ON5 HN5 0.3 1 0.0
|
||
CN7B CN7 ON5 HN5 0.8 3 0.0 ! RNA
|
||
CN7B CN7 ON5 HN5 0.5 1 0.0 ! RNA
|
||
! Was simply transfered from HN7 CN7 ON2 P
|
||
! adm jr. should convert to alcohol term (see ribose etc)
|
||
HN7 CN7 ON5 HN5 0.0 3 0.0
|
||
HN7 CN7 CN8B HN8 0.195 3 0.0 !gam H-C4'-C5'-H
|
||
HN7 CN7 CN7 CN8B 0.195 3 0.0 !gam H-C3'-C4'-C5'
|
||
!@@@@@@ End of torsions involving exocyclic atoms:
|
||
!@@@@@@ Begining of torsions for endocyclic atoms only:
|
||
CN8 CN7B ON6 CN7 0.6 6 180.0 !C2'-C1'-O4'-C4'
|
||
CN8 CN7 CN7 ON6 1.0 4 0.0 ! adm, 2011 DNA update new param, C2'-C3'-C4'-O4'; lowers c3'endo
|
||
CN8 CN7 CN7 ON6 0.3 5 180.0 ! adm, 2011 DNA update new param, C2'-C3'-C4'-O4'; position of minima
|
||
CN8 CN7 CN7 ON6 0.3 6 180.0 ! adm, 2011 DNA update new param, C2'-C3'-C4'-O4'; position of minima
|
||
CN7B CN7B ON6B CN7 0.0 6 0.0 ! RNA, Lowers barrier
|
||
CN7B CN7 CN7 ON6B 0.0 3 0.0 ! RNA
|
||
!======== CN7 CN8 CN7B ON6 for nucleosides, transfered from =========
|
||
!======== CN7 CN8 CN8 ON6 from thfoh ==============================
|
||
CN7 CN8 CN7B ON6 0.6 6 0.0 ! C3'-C2'-C1'-O4', adjust barrier
|
||
CN7 CN7B CN7B ON6B 0.4 6 0.0 ! RNA
|
||
!======== C1'-C2'-C3'-C4' ========
|
||
CN7B CN8 CN7 CN7 0.4 6 0.0 ! good for amplitudes
|
||
CN7B CN7B CN7 CN7 0.0 6 0.0 ! RNA
|
||
!======== CN7 CN7 ON6 CN7B for nucleosides, transfered from ========
|
||
!======== CN7 CN7 ON6 CN8 from thfohch3 ============================
|
||
CN7 CN7 ON6 CN7B 0.6 6 180.0 ! C3'-C4'-O4'-C1'
|
||
CN7 CN7 ON6B CN7B 0.0 6 180.0 ! RNA
|
||
!======== Directly adjusted with TM3P
|
||
HN7 CN7 CN7 CN8 0.0 3 0.0 !puc,H-C3'-C4'-C5'
|
||
!======== HN7 CN7 CN7 ON6 = H-C2'-C3'-O4'
|
||
HN7 CN7 CN8 CN7B 0.195 3 0.0 !H-C3'-C2'-C1'
|
||
HN7 CN7B CN8 CN7 0.195 3 0.0 !H-C1'-C2'-C3'
|
||
HN7 CN7 CN7 ON6 0.195 3 180.0 ! useful
|
||
HN8 CN8 CN7B ON6 0.195 3 0.0 !H-C2'-C1'-O4'
|
||
HN7 CN7 CN7 HN7 0.195 3 0.0 !H-C4'-C3'-H
|
||
HN7 CN7B CN8 HN8 0.195 3 0.0 !H-C1'-C2'-H
|
||
HN7 CN7 CN8 HN8 0.195 3 0.0 !H-C3'-C2'-H
|
||
HN8 CN8 CN7 CN7 0.195 3 0.0 ! useful *cccc*
|
||
HN7 CN7 ON6 CN7B 0.195 3 0.0 !H-C3'-C2'-C1'
|
||
HN7 CN7B ON6 CN7 0.000 3 0.0 !H-C1'-O4'-C4'
|
||
HN7 CN7 CN7 ON6B 0.195 3 180.0 ! RNA
|
||
HN9 CN9 CN7 ON6B 0.195 3 180.0 ! RNA, 5MET
|
||
HN8 CN8 CN7B ON6B 0.195 3 0.0 ! RNA
|
||
HN7 CN7B ON6B CN7 0.000 3 0.0 ! RNA
|
||
HN7 CN7 ON6B CN7B 0.195 3 0.0 ! RNA
|
||
HN7 CN7 CN7B CN7B 0.195 3 0.0 ! RNA, H-C3'-C2'-C1'
|
||
HN7 CN7B CN7B CN7 0.195 3 0.0 ! RNA, H-C1'-C2'-C3'
|
||
HN7 CN7B CN7B ON6B 0.195 3 0.0 ! RNA, H-C2'-C1'-O4'
|
||
!@@@@@@ End of torsions for endocyclic atoms only
|
||
|
||
!@@@@@@ Begining of torsions specifically defined for RNA @@@@@@
|
||
! N9-C1'-C2'-O2':
|
||
NN2 CN7B CN7B ON5 0.000 3 0.0 ! Adenine and cytosine
|
||
NN2B CN7B CN7B ON5 0.000 3 0.0 ! Guanine and uracil
|
||
ON5 CN7B CN7B HN7 0.000 3 0.0 !
|
||
HN7 CN7B CN7B HN7 0.000 3 0.0 !
|
||
CN7 CN7 CN7B ON5 0.000 3 0.0
|
||
ON6B CN7B CN7B ON5 0.000 3 0.0
|
||
ON5 CN7B CN7 ON2 0.000 3 0.0
|
||
! for ndph
|
||
ON5 CN7 CN7B ON2 0.000 3 0.0
|
||
ON5 CN7B CN7 ON5 0.000 3 0.0
|
||
HN7 CN7B ON5 HN5 0.000 3 0.0
|
||
!ejd, 2010 RNA update
|
||
HN5 ON5 CN7B CN7B 0.000 6 180.0 ! ejd, 2010 RNA update
|
||
HN5 ON5 CN7B CN7B 0.400 3 0.0 ! shifts min, ejd, 2010 RNA update
|
||
HN5 ON5 CN7B CN7B 0.400 2 0.0 ! ejd, 2010 RNA update
|
||
HN5 ON5 CN7B CN7B 0.800 1 0.0 ! height of right barrier and can shift min, ejd, 2010 RNA update
|
||
!to C3'
|
||
HN5 ON5 CN7B CN7 0.200 3 0.0 ! ejd, 2010 RNA update
|
||
HN5 ON5 CN7B CN7 0.000 2 180.0 ! ejd, 2010 RNA update
|
||
HN5 ON5 CN7B CN7 2.000 1 0.0 ! height of left side barrier, ejd, 2010 RNA update
|
||
!@@@@@@ End of torsions specifically defined for RNA @@@@@@
|
||
|
||
!Collection of parameters that were previously incorrectly categorized or labeled
|
||
CN7B ON6 CN7 CN9 0.0 3 0.0 ! added for sugar model compounds
|
||
HN7 CN7 CN7B ON5 0.195 3 0.0 ! for nadp/nadph (NOT!), adm jr.
|
||
HN7 CN7B CN7 CN7 0.195 3 0.0 ! for nadp/nadph (NOT!), adm jr.
|
||
HN7 CN7 CN7 CN7B 0.195 3 0.0 ! for nadp/nadph (NOT!), adm jr.
|
||
HN7 CN7 CN7B HN7 0.195 3 0.0 ! for nadp/nadph (NOT!), adm jr.
|
||
!from nad_ppi stream file
|
||
! pyrophosphate (ppi)
|
||
P3 ON2 P ON2 0.03 2 0.0 !nad/ppi, jjp1/adm jr. 7/95
|
||
P3 ON2 P ON2 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95
|
||
P ON2 P3 ON2 0.03 2 0.0 !nad/ppi, jjp1/adm jr. 7/95
|
||
P ON2 P3 ON2 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95
|
||
P3 ON2 P3 ON2 0.03 2 0.0 !nad/ppi, jjp1/adm jr. 7/95
|
||
P3 ON2 P3 ON2 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95
|
||
P ON2 P ON2 0.03 2 0.0 !nad/ppi, jjp1/adm jr. 7/95
|
||
P ON2 P ON2 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95
|
||
P ON2 P ON3 0.10 2 0.0 !nad/ppi, jjp1/adm jr. 7/95
|
||
P ON2 P ON3 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95
|
||
P ON2 P3 ON3 0.10 2 0.0 !nad/ppi, jjp1/adm jr. 7/95
|
||
P ON2 P3 ON3 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95
|
||
P3 ON2 P ON3 0.10 2 0.0 !nad/ppi, jjp1/adm jr. 7/95
|
||
P3 ON2 P ON3 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95
|
||
P3 ON2 P3 ON3 0.10 2 0.0 !nad/ppi, jjp1/adm jr. 7/95
|
||
P3 ON2 P3 ON3 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95
|
||
! protonated pyrophosphate (ppi2)
|
||
P ON2 P4 ON2 0.03 2 0.0 !from P ON2 P2 ON2, adm jr. 7/01
|
||
P ON2 P4 ON2 0.03 3 0.0 !from P ON2 P2 ON2, adm jr. 7/01
|
||
P4 ON2 P ON2 0.03 2 0.0 !from P ON2 P2 ON2, adm jr. 7/01
|
||
P4 ON2 P ON2 0.03 3 0.0 !from P ON2 P2 ON2, adm jr. 7/01
|
||
P ON2 P4 ON3 0.10 2 0.0 !from P ON2 P2 ON3, adm jr. 7/01
|
||
P ON2 P4 ON3 0.03 3 0.0 !from P ON2 P2 ON3, adm jr. 7/01
|
||
P4 ON2 P ON3 0.10 2 0.0 !from P ON2 P2 ON3, adm jr. 7/01
|
||
P4 ON2 P ON3 0.03 3 0.0 !from P ON2 P2 ON3, adm jr. 7/01
|
||
P ON2 P4 ON4 0.10 2 0.0 !from P ON2 P2 ON4, adm jr. 7/01
|
||
P ON2 P4 ON4 0.03 3 0.0 !from P ON2 P2 ON4, adm jr. 7/01
|
||
X ON4 P4 X 0.30 3 0.0 !from MP_1, adm jr.
|
||
|
||
IMPROPER
|
||
!
|
||
!V(improper) = Kpsi(psi - psi0)**2
|
||
!
|
||
!Kpsi: kcal/mole/rad**2
|
||
!psi0: degrees
|
||
!note that the second column of numbers (0) is ignored
|
||
!
|
||
!atom types Kpsi psi0
|
||
!
|
||
!
|
||
HN2 X X NN2 1.0 0 0.0 !C, adm jr. 11/97
|
||
NN2B CN4 CN5 HN2 7.0 0 0.0 !G, adm jr. 11/97
|
||
HN1 X X NN1 4.0 0 0.0 !G, adm jr. 11/97
|
||
NN1 CN2 HN1 HN1 6.0 0 0.0 !A,C adm jr. 11/97
|
||
CN1 X X ON1 90.0 0 0.0 !U
|
||
CN1T X X ON1 90.0 0 0.0 !U
|
||
CN1 NN2G CN5G ON1 90.0 0 0.0 !G
|
||
CN1T NN2B NN2U ON1 110.0 0 0.0 !T/O2, adm jr. 11/97
|
||
CN1 NN2U CN3T ON1 90.0 0 0.0 !T/O4, adm jr. 11/97
|
||
CN1 X X ON1C 80.0 0 0.0 !C, par_32, adm jr. 10/2/91
|
||
CN2 X X NN1 90.0 0 0.0 !C,
|
||
CN2 NN3G NN2G NN1 40.0 0 0.0 !G
|
||
CN2 NN3A CN5 NN1 40.0 0 0.0 !A
|
||
CN2 NN3 CN3 NN1 60.0 0 0.0 !C,
|
||
CN9 X X CN3T 14.0 0 0.0 !T, adm jr. 11/97
|
||
|
||
! Wildcards used to minimize memory requirements
|
||
NONBONDED NBXMOD 5 ATOM CDIEL FSHIFT VATOM VDISTANCE VFSWITCH -
|
||
CUTNB 14.0 CTOFNB 12.0 CTONNB 10.0 EPS 1.0 E14FAC 1.0 WMIN 1.5
|
||
!
|
||
!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
|
||
!
|
||
!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
|
||
!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
|
||
!
|
||
!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
|
||
!
|
||
HN1 0.0 -0.0460 0.2245
|
||
HN2 0.0 -0.0460 0.2245
|
||
HN3 0.0 -0.046 1.1000 !adm jr. aromatic Hvdw
|
||
HN4 0.0 -0.0460 0.2245
|
||
HN5 0.0 -0.0460 0.2245
|
||
HN6 0.0 -0.0220 1.3200
|
||
HN7 0.0 -0.0220 1.3200
|
||
HN8 0.0 -0.0280 1.3400 ! Hydrogen bound to CN8
|
||
HN9 0.0 -0.0240 1.3400 ! Hydrogen bound to CN9
|
||
!
|
||
NN1 0.0 -0.20 1.85
|
||
NN2 0.0 -0.20 1.85
|
||
NN2B 0.0 -0.20 1.85 ! From NN2, for N9 in guanines
|
||
NN2G 0.0 -0.20 1.85
|
||
NN2U 0.0 -0.20 1.85
|
||
NN3 0.0 -0.20 1.85
|
||
NN3A 0.0 -0.20 1.85
|
||
NN3G 0.0 -0.20 1.85
|
||
NN4 0.0 -0.20 1.85
|
||
NN6 0.0 -0.20 1.85
|
||
!
|
||
ON1 0.0 -0.1200 1.70
|
||
ON1C 0.0 -0.1200 1.70
|
||
ON2 0.0 -0.1521 1.77
|
||
ON3 0.0 -0.1200 1.70
|
||
ON4 0.0 -0.1521 1.77
|
||
ON5 0.0 -0.1521 1.77
|
||
ON6 0.0 -0.1521 1.77
|
||
ON6B 0.0 -0.1521 1.77
|
||
!
|
||
! base ring C vdw param, 11/14/97, adm jr
|
||
CN1 0.0 -0.10 1.9000
|
||
CN1T 0.0 -0.10 1.9000
|
||
CN2 0.0 -0.10 1.9000
|
||
CN3 0.0 -0.09 1.9000
|
||
CN3T 0.0 -0.09 1.9000 ! T, adm jr.
|
||
CN4 0.0 -0.075 1.9000
|
||
CN5 0.0 -0.075 1.9000
|
||
CN5G 0.0 -0.075 1.9000
|
||
CN7 0.0 -0.02 2.275 0.0 -0.01 1.90 !equivalent to protein CT1
|
||
CN7B 0.0 -0.02 2.275 0.0 -0.01 1.90 !equivalent to protein CT1
|
||
! alkane optimized terms below, Yin and MacKerell, 1998, JCC, In press
|
||
CN8 0.0 -0.0560 2.010 0.0 -0.01 1.90 !
|
||
CN8B 0.0 -0.0560 2.010 0.0 -0.01 1.90 !
|
||
CN9 0.0 -0.0780 2.040 0.0 -0.01 1.90 !
|
||
!
|
||
P 0.0 -0.585 2.15
|
||
P2 0.0 -0.585 2.15
|
||
P3 0.0 -0.585 2.15 ! nad/ppi, jjp1/adm jr.
|
||
P4 0.0 -0.585 2.15 ! for PPI2, adm jr.
|
||
|
||
NBFIX
|
||
! Emin Rmin
|
||
! (kcal/mol) (A)
|
||
!
|
||
|
||
HBOND CUTHB 0.5 ! If you want to do hbond analysis (only), then use
|
||
! READ PARAM APPEND CARD
|
||
! to append hbond parameters from the file: par_hbond.inp
|
||
|
||
END
|