[gmx-users] topology and coordinate file not matching after grompp
Swagata Patra
swagataliza at gmail.com
Tue Feb 9 06:16:20 CET 2016
Hi gromacs users.
I am trying to simulate a protein is mixed solution of water and 25%
benzene using gromos force field.
I tried to follow the steps suggested on gromacs website.
Here are the commands that I used:
> pdb2gmx_d -f protein.pdb -o protein_processed.gro -water spce -ignh
> editconf_d -f protein_processed.gro -o protein_newbox.gro -c -d 1.0 -bt
cubic
> genbox_d -cp protein_newbox.gro -ci benz.gro -nmol 250 -o phase1.gro (I
got the .gro file using prodrg)
> genbox_d -cp phase1.gro -cs spc216.gro -o solvated.gro
I prepared the .gro and .itp file using PRODRG. As I want to simulate the
protein in 25% benzene that’s why I am adding 250 in –ci –nmol option.
After getting the solvated.gro file I edited topol.top file
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include benzene topology
#include "benz.itp"
; Include water topology
#include "gromos43a1.ff/spce.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include "gromos43a1.ff/ions.itp"
[ system ]
; Name
Protein in water
[ molecules ]
; Compound #mols
Protein_chain_A 1
PDB 250*6
SOL 7217
But when I am giving this command “grompp_d -f ions.mdp -c 1r50_solv.gro -p
topol.top -o ions.tpr” I am getting the following error
Fatal error:
number of coordinates in coordinate file (solvated.gro, 24888) does not
match topology (topol.top, 26388).
How will I solve the problem? Please help me out. Here I am attaching the
benzene .gro and .itp file.
--
Swagata Patra
M.Tech (Biotech)
JRF
IIT Guwahati
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