[gmx-users] Issue with protein-ligand simulation

[Bratin Kumar Das]

Hi
   The number of particles in .gro file and .Top file is not same...Because
you didn't add ligand topology to the topol.top...Check carefully..it's
very basic problem...

On Mon 5 Aug, 2019, 3:57 PM GAYATHRI S, <gayathri.s at iitb.ac.in> wrote:

> Dear all,
>
> I am trying to run a protein-ligand simulation as described in the
> tutorial by Justin Lemkul
>
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex_old/01_pdb2gmx.html
>
> However, while creating a unit cell using editconf command, I encounter a
> problem. The output file (box.gro) doesn't contain the ligand coordinates.
>
> The command doesn't give any error and runs smoothly.
>
> But, when I reach the energy minimization step, grompp command gives the
> "Number of coordinates in coordinate file does not match topology" error.
>
> Kindly suggest how to fix this issue.
>
> Thank you.
>
> Regards,
> Gayathri S.
>
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