[gmx-users] Re: topology error

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 10 16:21:25 CEST 2011

lina wrote:
> On Sat, Oct 8, 2011 at 3:10 PM, ITHAYARAJA <ithayaraja at gmail.com 
> <mailto:ithayaraja at gmail.com>> wrote:
>     only 59 particle variation found out of 230 ligand coordinates.
>     On 8 October 2011 12:22, ITHAYARAJA <ithayaraja at gmail.com
>     <mailto:ithayaraja at gmail.com>> wrote:
>         Dear Sir,
>         I am actually simulating my protein with its ligand so I
>         incorporated all ligand (3) coordinates to my protein .gro file
>         and placed its .itp file also. I used gromas96 43a1 force field.
>         I found following error when i was doing grompp for energy
>         minimization. I went through FAQ and checked all but i couldn't
>         find what exactly it was.
>         So, I attached that files to you. I need your help to solve this
>         Program grompp, VERSION 4.5.1
>         Source code file: grompp.c, line: 377
>         Fatal error:
>         number of coordinates in coordinate file (GR_b4ion.gro, 66074)
>                      does not match topology (GR.top, 66015)
> I used to count the atom numbers in .gro file and manually modify the 
> topology to make them match.

More generally, the contents of the [molecules] directive in the .top must 
always match the contents of the coordinate file in terms of the number of 
molecules and the order in which they are listed.  Some Gromacs programs (like 
genbox and genion) are capable of making automatic updates, but anything else 
(like ligands) will have to be done manually.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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