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

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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?

Thanks in advance
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