[gmx-users] coordinates obtained from the Automated Topology Builder

[Justin Lemkul]

On 1/3/13 7:11 AM, Ahmet yıldırım wrote:
> Dear users,
>
> I get topology (A.itp) and structure (A.gro) files of a ligand using
> Automated Topology Builder.
> A.gro file has optimised geometry. That is, the coordinates of the
> atoms have been changed according to the initial file .pdb.
> I am confused. When I do simulation related to protein-ligand
> interactions, which coordinates I use?
> Optimised coordinates obtained from the Automated Topology Builder or
> original coordinates in .pdb?
>

If you have a ligand in complex with a protein, and then an optimization is done 
in the absence of the restricting influence of the protein, you'll probably get 
very bad interactions.  Always use the original coordinates in these cases.

-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

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