[gmx-users] grompp

Venkat Reddy venkat4bt at gmail.com
Wed Jun 18 11:55:38 CEST 2014

Did you update the 2nd line of your gro file (sol.gro) after adding ligand

On Wed, Jun 18, 2014 at 12:32 PM, Meenakshi Rajput <ashi.rajput39 at gmail.com>

> Hi gromacs users
> I run the grompp command
> (grompp_d -v -f minim.mdp -c sol.gro -o min.tpr -p hsa.top)
>  to generate .tpr file but i got the following error
> Fatal error:
> number of coordinates in coordinate file (sol.gro, 140012)
>              does not match topology (hsa.top, 140027)
> When I opened gro file, only protein and sol molecules are seen in .gro
> file but no ligand molecules. I dont know why it is happening..
> Can anybody help me?
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With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras

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