[gmx-users] hi

SeungPyo Hong sp1020 at gmail.com
Thu Aug 16 04:13:09 CEST 2007

On 8/15/07, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> vinod kumar wrote:
> > Hi, gmx-users,
> >
> > HI , how to overcome this problem
> > the output after grompp if em.mdp ............
> >> fatal error : number of coordinates in coordinate file ( solvated.gro8655)
> >> does not match topology ( top.top 8657)
> >
> > i have made necessary changes in the .top file with respect to the out
> > put of genbox .
> It seems that you have either used a different .top file, or not changed
> it correctly. Go back a step and try again.
> Mark
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I sometimes have that problem when adding ligand with using Dundee server.
Checking the number of atoms in the .pdb(or .gro) file and its .itp file
might be helpful.
When using Dundee server they give you the .gro file with all the hydrogen
But they give you 3 .pdb file.

'God used beautiful mathematics in creating the world.'
-Paul Dirac
'But he created too many object.'
-Seungpyo Hong

Seungpyo Hong
Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea
Tel. (82)-18-372-2468
sphong_ at kaist.ac.kr
sp1020 at gmail.com
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