Dear all
I am doing simulation of membrane protein ,for this first i
did the concatanation of protein in lipid bilayer in proper orientation
after that I am using inflategro script of teleman sir
but after doing first step successfully I am getting problem in second step
i,e energy minimisation step.
problem is related with coordinate file which I putted with grompp and my
topology file which I have made like this-
Include forcefield parameters
#include "ffG53a6_lipid.itp"
; Include DMPC chain topology
#include "dmpc.itp"
; Include protein chain topologies
#include "tap-mod.itp"
#ifdef POSRES_PROTEIN
#include "tap-mod_pr.itp"
#endif
; Include generic topology for ions
#include "ions.itp"
[ system ]
; Name
Protein in DMPC bilayer
[ molecules ]
; Name number
Protein_X 1
DMPC 119
NA+ 1
And the problem I am getting like this--
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.12#
checking input for internal consistency...
processing topology...
Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
Generated 770 of the 2278 non-bonded parameter combinations
Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp
Excluding 3 bonded neighbours molecule type 'Protein_X'
Excluding 3 bonded neighbours molecule type 'DMPC'
Excluding 1 bonded neighbours molecule type 'NA+'
processing coordinates...
-------------------------------------------------------
Program grompp, VERSION 4.0.3
Source code file: grompp.c, line: 362
Fatal error:
number of coordinates in coordinate file (inflated_dmpc.gro, 13253)
does not match topology (inflated_dmpc.top, 15392)
-------------------------------------------------------
If anyone have idea about this problem please suggest me something to solve
this problem.
Thnks a lot in advance.
Nitu Sharma
School of life sciences.
Jawaherlal Nehru University
New Delhi , India
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