[gmx-users] fatal erroe in prorein-ligand comlex

Bikash Ranjan Sahoo bikash.bioinformatic at protein.osaka-u.ac.jp
Wed Dec 17 03:11:51 CET 2014

Dear Yaser,
Gro file is sensitive and you should update the number manually after
adding the ligand atoms to the protein.gro file. Check the first line of
your protein.gro and ligand.gro. In the complex.gro the first line should
be the summation of both. Gromacs does not perform it manually. Kindly chck
again and rerun the grompp.

Good luck

On Wednesday, December 17, 2014, Yaser Hosseini <
yaser.hosseini.biologist at gmail.com> wrote:

> hi gromacs users
> i got error in step four in protein-ligand complex how can i fix it:
> Fatal error:
> number of coordinates in coordinate file (solv.gro, 144131)
>              does not match topology (topol.top, 144171)
> when i want to ran this:
> grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr
> i add my ligand drg.gro in protein_processed.gro.
> beside i cant find conf.gro that you say in this toturial:
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex_old/02_topology.html
> thank you .
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Warm regards
Bikash Ranjan Sahoo
Sent from I Phone 5
Osaka, Japan

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