[gmx-users] Ligand coming out while trying Drug-enzyme tutorial

[vivek sharma]

HI Tsjerk,
Thanks for your reply. But, I can't see if it is going suddenly or
gradually.
What i can see is the ligand is away from the molecule after editing the gro
file with PRODRG output.

It seems liek PRODRG has modified the co-ordinates that places ligand away
from the protein.

~Vivek
2010/1/25 Tsjerk Wassenaar <tsjerkw at gmail.com>

> Hi Vivek,
>
> > Now when I am processing the modified .gro file to generate box, the
> ligand
> > and cofactor are going away from the protein molecule and I am not able
> to
> > analyze the complex.
>
> Gradually going away, or suddenly jumping?
>
> In the latter case, read up on periodic boundary conditions.
>
> Tsjerk
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> Computational Chemist
> Medicinal Chemist
> Neuropharmacologist
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