nitu sharma wrote:
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)
-------------------------------------------------------
The only way to answer this question is to look in the coordinate file, look in
the topology (not what you keep posting, but the actual .itp file(s) for your
protein, etc). There are several possible problems, but these are all just
guesses on my part:
1. You did the concatenation wrong, and you have duplicates of many of your
species. 119 DMPC lipids should correspond to 5474 atoms under a UA
representation. Is your protein really 10,000 atoms?
2. Why do you have NA+ present? InflateGRO should have stripped out everything
that was not protein or lipid. Even if it didn't, you don't need to add ions yet.
3. Do you have [ molecules ] sections in your .itp files? This can lead to
duplication in the topology.
-Justin
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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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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