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
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