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

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Jan 25 08:25:42 CET 2010

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 A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist

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