[gmx-users] Coordinates problem

[Justin Lemkul]

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

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================