* \\\\ CHARMM36 All-Hydrogen Nucleic Acid Parameter File //// * Alexander D. MacKerell Jr. and coworkers * April 2011 * All comments to the CHARMM web site: www.charmm.org parameter * set discussion forum * !2010/2011 additions ! ejd, 2010 RNA update ! adm, 2011 DNA update ! For DNA update, new atom type required for P of DNA. This required ! replication of a number of parameters and the creation of new ! patches, DEOX and DEO5, to convert RNA to DNA, such that previous ! CHARMM scripts to generate DNA will no longer work. Note that the ! atom type change to P3 ONLY applies to the phosphodester linkage in ! DNA and NOT to terminal phosphates, DMP etc. ! ! !references ! !NUCLEIC ACIDS ! !Hart, K., Foloppe, N., Baker, C.M., Denning, E.J., Nilsson, L. and !MacKerell Jr., A.D. “Optimization of the CHARMM additive force field !for DNA: Improved treatment of the BI/BII conformational !equilibrium,” Journal of Chemical Theory and Computation, 8:348–362, !2012, http://dx.doi.org/10.1021/ct200723y ! !Denning, E.J., Priyakumar, U.D., Nilsson, L., and MacKerell Jr., A.D., !“Impact of 2’-hydroxyl sampling on the conformational properties of !RNA: Update of the CHARMM all-atom additive force field for RNA,” !JCC, In Press, 2011, NIHMSID #272247 !Foloppe, N. and MacKerell, Jr., A.D. "All-Atom Empirical Force Field for !Nucleic Acids: 1) Parameter Optimization Based on Small Molecule and !Condensed Phase Macromolecular Target Data. JCC, 2000, 21: 86-104. ! !MacKerell, Jr., A.D. and Banavali, N. "All-Atom Empirical Force Field for !Nucleic Acids: 2) Application to Molecular Dynamics Simulations of DNA !and RNA in Solution. JCC, 2000, 21: 105-120. ! ATOMS MASS -1 HN1 1.00800 ! Nucleic acid amine proton MASS -1 HN2 1.00800 ! Nucleic acid ring nitrogen proton MASS -1 HN3 1.00800 ! Nucleic acid aromatic carbon proton MASS -1 HN4 1.00800 ! Nucleic acid phosphate hydroxyl proton MASS -1 HN5 1.00800 ! Nucleic acid ribose hydroxyl proton MASS -1 HN6 1.00800 ! Nucleic acid ribose aliphatic proton MASS -1 HN7 1.00800 ! Nucleic acid proton (equivalent to protein HA) MASS -1 HN8 1.00800 ! Bound to CN8 in nucleic acids/model compounds MASS -1 HN9 1.00800 ! Bound to CN9 in nucleic acids/model compounds MASS -1 CN1 12.01100 ! Nucleic acid carbonyl carbon MASS -1 CN1T 12.01100 ! Nucleic acid carbonyl carbon (T/U C2) MASS -1 CN2 12.01100 ! Nucleic acid aromatic carbon to amide MASS -1 CN3 12.01100 ! Nucleic acid aromatic carbon MASS -1 CN3T 12.01100 ! Nucleic acid aromatic carbon, Thy C5 MASS -1 CN4 12.01100 ! Nucleic acid purine C8 and ADE C2 MASS -1 CN5 12.01100 ! Nucleic acid purine C4 and C5 MASS -1 CN5G 12.01100 ! Nucleic acid guanine C5 MASS -1 CN7 12.01100 ! Nucleic acid carbon (equivalent to protein CT1) MASS -1 CN7B 12.01100 ! Nucleic acid aliphatic carbon for C1' MASS -1 CN8 12.01100 ! Nucleic acid carbon (equivalent to protein CT2) MASS -1 CN8B 12.01100 ! Nucleic acid carbon (equivalent to protein CT2) MASS -1 CN9 12.01100 ! Nucleic acid carbon (equivalent to protein CT3) MASS -1 NN1 14.00700 ! Nucleic acid amide nitrogen MASS -1 NN2 14.00700 ! Nucleic acid protonated ring nitrogen MASS -1 NN2B 14.00700 ! From NN2, for N9 in GUA different from ADE MASS -1 NN2U 14.00700 ! Nucleic acid protonated ring nitrogen, ura N3 MASS -1 NN2G 14.00700 ! Nucleic acid protonated ring nitrogen, gua N1 MASS -1 NN3 14.00700 ! Nucleic acid unprotonated ring nitrogen MASS -1 NN3A 14.00700 ! Nucleic acid unprotonated ring nitrogen, ade N1 and N3 MASS -1 NN3G 14.00700 ! Nucleic acid unprotonated ring nitrogen, gua N3 MASS -1 NN4 14.00700 ! Nucleic acid purine N7 MASS -1 NN6 14.00700 ! Nucleic acid sp3 amine nitrogen (equiv to protein nh3) MASS -1 ON1 15.99940 ! Nucleic acid carbonyl oxygen MASS -1 ON1C 15.99940 ! Nucleic acid carbonyl oxygen, cyt O2 MASS -1 ON2 15.99940 ! Nucleic acid phosphate ester oxygen MASS -1 ON3 15.99940 ! Nucleic acid =O in phosphate MASS -1 ON4 15.99940 ! Nucleic acid phosphate hydroxyl oxygen MASS -1 ON5 15.99940 ! Nucleic acid ribose hydroxyl oxygen MASS -1 ON6 15.99940 ! Nucleic acid deoxyribose ring oxygen MASS -1 ON6B 15.99940 ! Nucleic acid ribose ring oxygen MASS -1 P 30.97400 ! phosphorus MASS -1 P2 30.97400 ! phosphorus, adm, 2011 DNA update BONDS ! !V(bond) = Kb(b - b0)**2 ! !Kb: kcal/mole/A**2 !b0: A ! !atom type Kb b0 ! !2-(aminobutyl)-1,3-propandiol terms CN8 NN6 200.000 1.480 ! methylammonium NN6 HN1 403.000 1.040 ! methylammonium !abasic deoxynucleoside ON6 CN8B 260.0 1.420 ! susil CN8 CN8B 222.50 1.528 ! Alkanes, sacred ! CN1 CN3 302.0 1.409 !U, adm jr. 11/97 CN1 CN3T 302.0 1.403 !T, adm jr. 11/97 CN1 CN5G 302.0 1.360 !G, adm jr. 11/97 CN1 NN2 380.0 1.367 !C, adm jr. 11/97 CN1T NN2B 302.0 1.348 !U,T adm jr. 11/97 CN1 NN2G 340.0 1.396 !G, adm jr. 11/97 CN1 NN2U 340.0 1.389 !U,T adm jr. 11/97 CN1T NN2U 340.0 1.383 !U,T adm jr. 11/97 CN1 NN3 350.0 1.335 !C, adm jr. 11/97 CN1T ON1 860.0 1.230 !nad/ppi, jjp1/adm jr. 7/95 CN1 ON1 660.0 1.234 !U,A,G par_a4 adm jr. 10/2/91 CN1 ON1C 620.0 1.245 !C, adm jr. 10/2/91 CN2 CN3 320.0 1.406 !C, adm jr. 11/97 CN2 CN5 360.0 1.358 !A, adm jr. 11/97 CN2 NN1 360.0 1.366 !C,A,G JWK, adm jr. 10/2/91 CN2 NN2G 400.0 1.392 !G CN2 NN3 450.0 1.343 !C CN2 NN3A 400.0 1.342 !A, adm jr. 11/97 CN2 NN3G 320.0 1.326 !G, adm jr. 11/97 CN3 CN3 500.0 1.326 !C,U adm jr. 11/97 CN3 CN3T 560.0 1.320 !T, adm jr. 11/97 CN3T CN9 230.0 1.478 !T, adm jr. 11/97 CN3 HN3 350.0 1.09 !C,U, JWK CN3T HN3 350.0 1.09 !T, JWK CN3 NN2 302.0 1.343 !C, adm jr. 11/97 CN3 NN2B 320.0 1.343 !U,T adm jr. 11/97 CN4 HN3 380.0 1.09 !G,A, JWK par_a7 9/30/91 CN4 NN2 320.0 1.374 !A, adm jr. 11/97 CN4 NN2B 300.0 1.378 !G, adm jr. 11/97 CN4 NN3A 420.0 1.322 !A, adm jr. 11/97 CN4 NN4 400.0 1.305 !G,A, adm jr. 11/97 CN5 CN5 310.0 1.361 !A, adm jr. 11/97 CN5 CN5G 320.0 1.350 !G, adm jr. 11/97 CN5 NN2 300.0 1.375 !A, adm jr. 11/97 CN5 NN2B 302.0 1.375 !G, adm jr. 11/97 CN5 NN3A 350.0 1.312 !A, JWK par_a8 9/30/91 CN5 NN3G 350.0 1.315 !G, adm jr. 11/97 CN5 NN4 310.0 1.355 !A, adm jr. 11/97 CN5G NN4 310.0 1.365 !G, adm jr. 11/97 CN8 CN8 222.50 1.528 !Alkanes, sacred CN8 CN9 222.50 1.528 !Alkanes, sacred CN8 NN2 400.0 1.460 !9-E-GUA, ADM JR. CN8 ON5 428.0 1.42 !RIBOSE, MeOH CN9 HN9 322.0 1.111 !alkanes CN9 ON2 340.0 1.43 !DMP, ADM Jr. HN1 NN1 488.0 1.00 !A,C,G, JWK, adm jr. 7/24/91 HN2 NN2 474.0 1.01 !C,U, JWK HN2 NN2B 474.0 1.01 !G, adm jr. 11/97 HN2 NN2G 471.0 1.01 !G, JWK, par_a12 9/30/91 HN2 NN2U 474.0 1.01 !U, JWK, adm jr. 7/24/91 HN4 ON4 545.0 0.960 !MP_1, ADM Jr. ON2 P 270.0 1.60 !DMP, ADM Jr. ON2 P2 270.0 1.60 !DMP, ADM Jr., adm, 2011 DNA update ON3 P 580.0 1.48 !DMP, ADM Jr. ON3 P2 580.0 1.48 !DMP, ADM Jr., adm, 2011 DNA update ON4 P 237.0 1.58 !MP_1, ADM Jr. ON4 P2 237.0 1.58 !MP_1, ADM Jr., adm, 2011 DNA update !NN5 HN1 460.0 1.01 !sugar model, adm jr. !@@@@@@@@@ Begining of endocyclic bonds for deoxy-ribose @@@@@@@@@ CN7B ON6 260.0 1.420 ! From exp CN7B CN8 200.0 1.518 ! From exp CN7 ON6 240.0 1.446 ! Fom exp. CN7 CN7 222.5 1.529 ! From exp CN7 CN8 222.5 1.516 ! From exp. CN7 CN9 222.5 1.516 ! for 5MET, From alkanes CN7 HN7 309.0 1.111 !Alkanes, sacred CN8 HN8 309.0 1.111 !Alkanes, sacred CN7B HN7 309.0 1.111 ! From CN8 HN7 (NF) !@@@@@@@@@ End of endocyclic bonds for deoxy-ribose @@@@@@@@@ !@@@@@@@@@ Begining of endocyclic bonds for ribose @@@@@@@@@ CN7B ON6B 260.0 1.420 ! From CN7B ON6 CN7 ON6B 240.0 1.480 ! From CN7 ON6 CN7B CN7B 200.0 1.450 ! CN7 CN7B 222.5 1.460 ! Specific to RNA !@@@@@@@@@ End of endocyclic bonds for ribose @@@@@@@@@ !@@@@@@@@@ Begining of exocyclic bonds for deoxy-ribose @@@@@@@@@ CN7 CN8B 222.5 1.512 ! From exp. CN8B ON2 320.0 1.44 ! From exp !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 @@@@@@@@@ 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 ! 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. 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 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