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

Justin Lemkul jalemkul at vt.edu
Thu Jan 3 13:26:16 CET 2013

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


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