[gmx-users] topology and parameter set up
Jennifer Vo
quyviolet at gmail.com
Mon Feb 2 12:37:36 CET 2015
Dear Experts,
I am facing the problem of simulation of protein - ligand complex using
amber99sb force field.
Since I created a topol.top for the system
; Include forcefield parameters
#include "amber99sb.ff/forcefield.itp"
[ atomtypes ]
;name bond_type mass charge ptype sigma epsilon
Amb
CA CA 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ;
1.91 0.0860
H4 H4 0.00000 0.00000 A 2.51055e-01 6.27600e-02 ;
1.41 0.0150
HA HA 0.00000 0.00000 A 2.59964e-01 6.27600e-02 ;
1.46 0.0150
C C 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ;
1.91 0.0860
O O 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ;
1.66 0.2100
N N 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ;
1.82 0.1700
H H 0.00000 0.00000 A 1.06908e-01 6.56888e-02 ;
0.60 0.0157
N* N* 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ;
1.82 0.1700
CT CT 0.00000 0.00000 A 3.39967e-01 4.57730e-01 ;
1.91 0.1094
H2 H2 0.00000 0.00000 A 2.29317e-01 6.56888e-02 ;
1.29 0.0157
H1 H1 0.00000 0.00000 A 2.47135e-01 6.56888e-02 ;
1.39 0.0157
OH OH 0.00000 0.00000 A 3.06647e-01 8.80314e-01 ;
1.72 0.2104
HO HO 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ;
0.00 0.0000
OS OS 0.00000 0.00000 A 3.00001e-01 7.11280e-01 ;
1.68 0.1700
P P 0.00000 0.00000 A 3.74177e-01 8.36800e-01 ;
2.10 0.2000
O2 O2 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ;
1.66 0.2100
CK CK 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ;
1.91 0.0860
H5 H5 0.00000 0.00000 A 2.42146e-01 6.27600e-02 ;
1.36 0.0150
NB NB 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ;
1.82 0.1700
CB CB 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ;
1.91 0.0860
N2 N2 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ;
1.82 0.1700
NC NC 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ;
1.82 0.1700
CQ CQ 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ;
1.91 0.0860
; Include chain topologies
#include "A.itp"
; Include Position restraint file
#ifdef POSRES
#include "posre_A.itp"
#endif
; Include chain topologies
#include "B.itp"
; Include Position restraint file
#ifdef POSRES
#include "posre_B.itp"
#endif
; Include custom ligand topologies
#include "npd.itp"
; Ligand position restraints
#ifdef POSRES_LIG
#include "posre_npd.itp"
#endif
; Include water topology
#include "amber99sb.ff/tip3p.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include generic ion topology
#include "amber99sb.ff/ions.itp"
[ system ]
; Name
system in water
[ molecules ]
; Compound #mols
A 1
B 1
NPD 1
SOL 42322
NA 24
The Protein and the Ligand were under energy minimization and a short MD
separatedly to be sure there is no problem with the topology. But when I
merge two topol.top from protein and from ligand, the error came at NPT
step after successfully energy minimization and NVT
"This is likely either a 1,4 interaction, or a listed interaction inside a
smaller molecule you are decoupling during a free energy calculation. Since
interactions at distances beyond the table cannot be computed, they are
skipped until they are inside the table limit again. You will only see this
message once, even if it occurs for several interactions.
IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason."
This is NPT.mdp
title = system in water
define = -DPOSRES -DPOSRES_LIG ; position restrain the protein
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 500000 ; 2 * 500000 = 1000 ps, 1 ns
dt = 0.002 ; 2 fs
; Output control
nstxout = 5000 ; save coordinates every 1.0 ps
nstvout = 5000 ; save velocities every 1.0 ps
nstenergy = 500 ; save energies every 1.0 ps
nstlog = 500 ; update log file every 1.0 ps
energygrps = Protein NPD
; Bond parameters
continuation = yes ; Restarting after NVT
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
;ns_type = grid ; search neighboring grid cels
;nstlist = 5 ; 10 fs
;rlist = 1.4 ; short-range neighborlist cutoff (in nm)
;rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm)
;rvdw = 1.4 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for
long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein_NPD Water_and_ions ; two coupling groups -
more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300 ; reference temperature, one for
each group, in K
; Pressure coupling is on
pcoupl = Berendsen ; Pressure coupling on in NPT
pcoupltype = isotropic ; uniform scaling of
box vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure,
in bar
compressibility = 4.5e-5 ; isothermal compressibility of
water, bar^-1
refcoord_scaling = com
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no ; Velocity generation is off
I do appreciate for any help.
Regards,
Jennifer
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