[gmx-users] grompp error no. of coordinate file doesn't match with topology file

Justin A. Lemkul jalemkul at vt.edu
Thu Apr 16 12:39:14 CEST 2009



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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