[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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