Dear Gromacs users, I am new to gromacs. I have just installed and read some tutorials. I would like to start reproducing the results I have calculated with another program (Dynamo). My system has a protein, water, ATP and N-acetylglutamate (NAG). The protein and water are trivial to convert. But I would like to use the same ATP and NAG parameters that I already have in my OPLS file (I enclose this file for the ATP at the end of the mail). I know PRODRG can generate the topology files, but it also creates the force field parameters, doesn't it? Is there an automatic way to translate the OPLS format to gromacs? Or could you suggest another work-around? Thanks in advance, Ramon
!=============================================================================== ! OPLS MM Definition File for ATP !=============================================================================== ! ! . Notes: ! ! !=============================================================================== MM_Definitions OPLS_AA 1.0 ! . Atom Type Definitions. Types ! Atom Name Atomic Number Sigma Epsilon H 1 0.00000 0.00000 HO 1 0.00000 0.00000 HC 1 2.50000 0.03000 CA 6 3.50000 0.08000 ! for Adenine CB 6 3.50000 0.08000 ! for Adenine CK 6 3.50000 0.08000 ! for Adenine CQ 6 3.50000 0.08000 ! for Adenine CT 6 3.50000 0.06600 N* 7 3.25000 0.17000 N2 7 3.25000 0.17000 NB 7 3.25000 0.17000 ! for Adenine NC 7 3.25000 0.17000 ! for Adenine O 8 3.15000 0.20000 OH 8 3.07000 0.17000 OS 8 2.90000 0.14000 P 15 3.74000 0.20000 End ! . Electrostatics and Lennard-Jones Options. Electrostatics Scale 0.5 Lennard_Jones Scale 0.5 ! . Units specification. Units kcal/mole !=============================================================================== ! . Residue Definitions. !=============================================================================== Residues !------------------------------------------------------------------------------- Residue ATP !------------------------------------------------------------------------------- ! # Atoms, bonds and impropers. 44 45 5 N1 NC -0.53 ! Impact Adenine C2 CQ 0.22 ! Impact Adenine H2 HC 0.20 ! Impact Adenine N3 NC -0.55 ! Impact Adenine C4 CB 0.38 ! Impact Adenine C5 CB 0.15 ! Impact Adenine C6 CA 0.44 ! Impact Adenine N7 NB -0.49 ! Impact Adenine C8 CK 0.20 ! Impact Adenine H8 HC 0.20 ! Impact Adenine N9 N* -0.50 ! Impact Adenine N10 N2 -0.81 ! Impact Adenine H11 H 0.37 ! Impact Adenine H12 H 0.37 ! Impact Adenine C1' CT 0.25 ! adjusted H1' HC 0.10 ! Impact HC hemiacetal C2' CT 0.20 ! Impact CT diols H2' HC 0.10 ! Impact HC hemiacetal O2' OH -0.70 ! Impact OH6 hemiacetal, diol HT2' HO 0.43 ! Impact HO hemiacetal, diol C3' CT 0.20 ! Impact CT diols H3' HC 0.10 ! Impact HC hemiacetal O3' OH -0.70 ! Impact OH6 hemiacetal, diol HT3' HO 0.43 ! Impact HO hemiacetal, diol C4' CT 0.24 ! adjusted O4' OS -0.40 ! Impact OS ether, acetal. H4' HC 0.10 ! Impact HC hemiacetal C5' CT 0.42 ! HF/6-31+G* CHelpG H51' HC -0.10 ! HF/6-31+G* CHelpG H52' HC -0.10 ! HF/6-31+G* CHelpG O5' OS -0.71 ! HF/6-31+G* CHelpG PA P 1.85 ! HF/6-31+G* CHelpG OA1 O -1.07 ! HF/6-31+G* CHelpG OA2 O -1.07 ! HF/6-31+G* CHelpG OA3 OS -0.78 ! HF/6-31+G* CHelpG PB P 1.98 ! HF/6-31+G* CHelpG OB1 O -1.09 ! HF/6-31+G* CHelpG OB2 O -1.09 ! HF/6-31+G* CHelpG OB3 OS -0.74 ! HF/6-31+G* CHelpG PG P 2.04 ! HF/6-31+G* CHelpG OG1 O -1.18 ! HF/6-31+G* CHelpG OG2 O -1.18 ! HF/6-31+G* CHelpG OG3 O -1.18 ! HF/6-31+G* CHelpG N1 C2 ; C2 N3 ; C2 H2 ; N3 C4 ; C4 C5 ; C5 C6 C6 N1 ; C6 N10 ; N10 H11 ; N10 H12 ; C5 N7 ; N7 C8 C8 N9 ; C8 H8 ; N9 C4 ; N9 C1' ; C1' C2' ; C1' H1' C2' C3' ; C2' H2' ; C2' O2' ; O2' HT2'; C3' C4' ; C3' H3' C3' O3' ; O3' HT3'; C4' C5' ; C4' H4' ; C4' O4' ; O4' C1' C5' O5' ; C5' H51'; C5' H52'; O5' PA ; PA OA1 ; PA OA2 PA OA3 ; OA3 PB ; PB OB1 ; PB OB2 ; PB OB3; OB3 PG PG OG1 ; PG OG2 ; PG OG3 N1 N3 C2 H2 ; N1 C5 C6 N10 ; N3 C5 C4 N9 C4 C6 C5 N7 ; N7 N9 C8 H8 !=============================================================================== ! . Parameter Definitions. !=============================================================================== Parameters Bonds ! Atoms FC Equil. CT HC 340.0 1.090 CT N* 337.0 1.475 CT CT 268.0 1.529 CT OH 320.0 1.410 CT OS 320.0 1.410 H N2 434.0 1.010 HO OH 553.0 0.945 OS P 230.0 1.610 O P 525.0 1.480 CA CB 469.0 1.404 ! for Adenine CA NC 483.0 1.339 ! for Adenine CA N2 481.0 1.340 ! for Adenine CB CB 520.0 1.370 ! for Adenine CB N* 436.0 1.374 ! for Adenine CB NB 414.0 1.391 ! for Adenine CB NC 461.0 1.354 ! for Adenine CK NB 529.0 1.304 ! for Adenine CK N* 440.0 1.371 ! for Adenine CK HC 340.0 1.080 ! for Adenine CQ HC 367.0 1.080 ! for Adenine CQ NC 502.0 1.324 ! for Adenine End Angles ! Atoms FC Equil. CB CA N2 70.0 123.50 ! for Adenine CB CA NC 70.0 117.30 ! for Adenine N2 CA NC 70.0 119.30 ! for Adenine CA CB CB 85.0 117.30 ! for Adenine CA CB NB 70.0 132.40 ! for Adenine CB CB N* 70.0 106.20 ! for Adenine CB CB NB 70.0 110.40 ! for Adenine CB CB NC 70.0 127.70 ! for Adenine N* CB NC 70.0 126.20 ! for Adenine N* CK NB 70.0 113.90 ! for Adenine HC CK NB 35.0 120.00 ! for Adenine HC CK N* 35.0 120.00 ! for Adenine CT CT CT 58.35 109.50 ! Theta(eq) modified. CT CT OH 50.0 109.50 CT CT OS 50.0 109.50 CT CT N* 50.0 109.50 CT CT HC 37.5 110.70 HC CT HC 33.0 107.80 HC CT N* 35.0 109.50 HC CT OH 35.0 109.50 HC CT OS 35.0 109.50 N* CT OS 50.0 109.50 HC CQ NC 35.0 115.45 NC CQ NC 70.0 129.10 CB N* CK 70.0 105.40 ! for Adenine CB N* CT 70.0 125.80 ! from bill2 (modified) CK N* CT 70.0 128.80 ! from bill2 (modified) CA N2 H 35.0 120.00 ! for Adenine H N2 H 35.0 120.00 ! from H2 N2 H2 CB NB CK 70.0 103.80 ! for Adenine CA NC CQ 70.0 118.60 ! for Adenine CB NC CQ 70.0 111.00 ! for Adenine CT OS CT 60.0 109.50 CT OS P 100.0 120.50 CT OH HO 55.0 108.50 O P O 140.0 119.90 ! for O2-P -O2 Nat. O P OS 100.0 108.23 ! for O2-P -OS Nat. OS P OS 45.0 102.60 P OS P 100.0 125.00 ! Theta(eq) from the x-ray structure End Dihedrals ! Atoms V0 V1 V2 V3 CA CB CB N* 0.000 0.000 7.250 0.000 ! Impact X-CB-CB-X (aromatic ring) CA CB CB NC 0.000 0.000 7.250 0.000 ! Impact X-CB-CB-X (aromatic ring) NC CB CB NB 0.000 0.000 7.250 0.000 ! Impact X-CB-CB-X (aromatic ring) NB CB CB N* 0.000 0.000 7.250 0.000 ! Impact X-CB-CB-X (aromatic ring) CA CB NB CK 0.000 0.000 7.250 0.000 ! Impact X-CB-NB-X (aromatic ring) CB CB CA NC 0.000 0.000 7.250 0.000 ! Impact X-CB-CA-X (aromatic ring) CB CA NC CQ 0.000 0.000 7.250 0.000 ! Impact X-CA-NC-X (aromatic ring) CB CB NC CQ 0.000 0.000 7.250 0.000 ! Impact X-CB-NC-X (aromatic ring) CB CB NB CK 0.000 0.000 7.250 0.000 ! Impact X-CB-NB-X (aromatic ring) CB CB N* CK 0.000 0.000 7.250 0.000 ! Impact X-CB-NA-X (aromatic ring) CB NC CQ NC 0.000 0.000 7.250 0.000 ! Impact X-CQ-NC-X (aromatic ring) CA NC CQ NC 0.000 0.000 7.250 0.000 ! Impact X-CQ-NC-X (aromatic ring) CB NB CK N* 0.000 0.000 7.250 0.000 ! Impact X-CK-NB-X (aromatic ring) NC CA CB NB 0.000 0.000 7.250 0.000 ! Impact X-CB-CA-X (aromatic ring) N* CB NC CQ 0.000 0.000 7.250 0.000 ! Impact X-CB-NC-X (aromatic ring) NB CK N* CB 0.000 0.000 7.250 0.000 ! Impact X-CK-NA-X (aromatic ring) NC CB N* CK 0.000 0.000 7.250 0.000 ! Impact X-CB-NA-X (aromatic ring) HC CQ NC CA 0.000 0.000 7.250 0.000 ! Impact X-CQ-NC-X (aromatic ring) HC CQ NC CB 0.000 0.000 7.250 0.000 ! Impact X-CQ-NC-X (aromatic ring) HC CK NB CB 0.000 0.000 7.250 0.000 ! Impact X-CK-NB-X (aromatic ring) HC CK N* CB 0.000 0.000 7.250 0.000 ! Impact X-CK-NA-X (aromatic ring) HC CK N* CT 0.000 0.000 7.250 0.000 ! Impact X-CK-NA-X (aromatic ring) CT N* CB CB 0.000 0.000 7.250 0.000 ! Impact X-CB-NA-X (aromatic ring) CT N* CB NC 0.000 0.000 7.250 0.000 ! Impact X-CB-NA-X (aromatic ring) CT N* CK NB 0.000 0.000 7.250 0.000 ! Impact X-CK-NA-X (aromatic ring) N2 CA NC CQ 0.000 0.000 7.250 0.000 ! Impact X-CA-NC-X (aromatic ring) N2 CA CB CB 0.000 0.000 7.250 0.000 ! Impact X-CB-CA-X (aromatic ring) N2 CA CB NB 0.000 0.000 7.250 0.000 ! Impact X-CB-CA-X (aromatic ring) NC CA N2 H 0.000 1.400 0.000 0.000 ! Impact NC-CA-N2-H (Adenine RZ) CB CA N2 H 0.000 0.000 1.400 0.000 ! Impact CB-CA-N2-H (adenine RZhou) OH CT CT N* 0.000 9.508 0.000 0.000 ! for sug-nucl (from diols) CT OS CT N* 0.000 -0.500 -1.500 1.000 ! Impact N?-CT-OS-CT (imidazoles, indoles, purines) CK N* CT OS 0.000 -1.500 -1.500 0.000 ! Impact CK-N*-CT-OS (imidazoles, indoles, purines) CB N* CT OS 0.000 1.500 -1.500 0.000 ! Impact C?-N*-CT-OS (imidazoles, indoles, purines) CT CT N* CB 0.000 1.000 -0.350 0.000 ! Impact C?-N*-CT-CT (imidazoles, indoles, purines) CT CT N* CK 0.000 -1.000 -0.350 0.000 ! Impact CK-N*-CT-CT (imidazoles, indoles, purines) HC CT N* CB 0.000 1.000 -0.350 0.000 ! Impact C?-N*-CT-CT (imidazoles, indoles, purines) HC CT N* CK 0.000 -1.000 -0.350 0.000 ! Impact CK-N*-CT-CT (imidazoles, indoles, purines) CT CT CT N* 0.000 2.732 -0.229 0.485 ! Impact CT-CT-CT-NA (rzhou's best guess) HC CT CT N* 0.000 2.732 -0.229 0.485 ! Impact CT-CT-CT-NA (rzhou's best guess) CT CT CT CT 0.000 1.300 -0.050 0.200 ! Impact CT-CT-CT-CT (hydrocarbon all-atom) HC CT CT OH 0.000 0.000 0.000 0.468 ! Impact HC-CT-CT-OH2 (alcohols, ethers AA) HC CT CT OS 0.000 0.000 0.000 0.468 ! Impact HC-CT-CT-OS (alcohols, ethers AA) HC CT CT HC 0.000 0.000 0.000 0.300 ! Impact HC-CT-CT-HC (hydrocarbon all-atom) HC CT CT CT 0.000 0.000 0.000 0.300 ! Impact HC-CT-CT-CT (hydrocarbon all-atom) CT CT CT OH 1.552 -1.552 0.000 0.000 ! Impact CT-CT-CT-OH2 (polyols AA) CT CT CT OS 0.000 1.711 -0.500 0.663 ! Impact CT-CT-CT-OS (alcohols, ethers AA) OH CT CT OH 0.000 9.508 0.000 0.000 ! Impact OH2-CT-CT-OH2 (diols only AA) OS CT CT OH 0.000 4.319 0.000 0.000 ! Impact OH2-CT-CT-OS (rzhou 07/98) OS CT CT OS 0.000 4.319 0.000 0.000 ! Impact OH2-CT-CT-OS (rzhou 07/98) CT CT OH HO 0.000 -0.356 -0.174 0.492 ! Impact CT-CT-OH2-HO (alcohols AA) HC CT OH HO 0.000 0.000 0.000 0.450 ! Impact HC-CT-OH2-HO (alcohols AA) CT OS CT CT 0.000 0.650 -0.250 0.670 ! Impact CT-OS-CT-CT (ethers AA) HC CT OS CT 0.000 0.000 0.000 0.760 ! Impact HC-CT-OS-CT (ethers AA) HC CT OS P 0.000 0.000 0.000 0.357 ! Impact P2-OS-CT-HC (MeOPO3 (-2) mll) CT CT OS P 0.000 0.000 0.000 0.357 ! Impact P2-OS-CT-HC (MeOPO3 (-2) mll) CT OS P OS 0.000 0.000 0.000 0.562 ! Impact O2-P2-OS-CT (MeOPO3 (-2) mll) CT OS P O 0.000 0.000 0.000 0.562 ! Impact O2-P2-OS-CT (MeOPO3 (-2) mll) P OS P O 0.000 0.000 0.000 0.000 ! Better results P OS P OS 0.000 0.000 0.000 0.000 ! Better results End Impropers ! Atoms V0 V1 V2 V3 NC NC CQ HC 0.000 0.000 1.100 0.000 ! for Adenine (from CA CA CA HA) NB N* CK HC 0.000 0.000 1.100 0.000 ! " " " NC CB CA N2 0.000 0.000 1.100 0.000 ! " " " NC CB CB N* 0.000 0.000 1.100 0.000 ! for Adenine (from CA CA CA CT) CB CA CB NB 0.000 0.000 1.100 0.000 ! " " " CK CB N* CT 0.000 0.000 1.100 0.000 ! ADE-SUG End End End _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php