[gmx-users] Converting OPLS parameters
Ramon Crehuet
rcsqtc at iiqab.csic.es
Thu Apr 24 15:13:22 CEST 2008
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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