[gmx-users] Converting OPLS parameters
Ran Friedman
r.friedman at bioc.uzh.ch
Thu Apr 24 16:34:02 CEST 2008
Hello Ramon,
There's no automatic way, and prodrg doesn't deal with OPLS. If you have
common residues (protein, water, maybe also ATP and NAG) you can use
pdb2gmx. Otherwise, you'll have to write a script or do things by hand.
Since you already have the parameters it shouldn't be too difficult.
Ran.
Ramon Crehuet wrote:
> 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
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--
------------------------------------------------------
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Email: r.friedman at bioc.unizh.ch
Skype: ran.friedman
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