[gmx-users] Coordinates problem

Justin Lemkul jalemkul at vt.edu
Tue Dec 4 20:25:02 CET 2012

On 12/4/12 1:37 PM, Marcelo Depolo wrote:
> Hi everyone!
> I'm running a protein-ligand simulation and i'm having a little problem
> with the ligand atoms coordinates. After I equilibrate the simulation box
> with counter-ions, i checked my ligand with VMD and it was ok. After a
> minimization process, a hydrogen atom and a oxygen atom occupies the same
> xyz coordinates. This can be verified in a highFmax value obtained in the
> minimization (2.16717723680607e+06 on atom 3881)
> Just for record, I already included the ligand coordinates in the .gro file
> and its topology (.itp) in .top file before I even fill the box with water.
> Can someone help me?

Check the topology - does the ligand successfully minimize by itself in vacuo? 
If it does, then the topology is sound and there's something wrong with how the 
ligand is placed within the protein.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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