[gmx-users] Coordinates problem

Marcelo Depolo marcelodepolo at gmail.com
Tue Dec 4 19:37:34 CET 2012

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?

Marcelo Depólo Polêto
Molecular Animal Infectology Laboratory - LIMA
Department of Biochemistry and Molecular Biology
Universidade Federal de Viçosa - UFV -

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