On Sat, May 30, 2009, Workalemhu Berhanu wrote:
> I am working on peptide from pdb and I had my ligand (aromatic organic
> molecule, for which I created the topology and coordinate file using
> GAFF). My goal is to get the complex of the peptide and my ligand
> and run molecular dynamic simulation on the complex. I docked my
> ligand to my peptide and to create the topology and coordinate file for
> the complex I tried to use GAFF and I got the following error. Would
> please please help me in figure out what is wrong with my approach to
> my problem? Can you please tell me a step I should follow if mine is
> wrong? Thank you very much in advance.
First, antechamber is designed to run on single residues or on drug-like
molecules. If you have a peptide as part of your system, you should use the
standard Amber force fields to model it, and just use antechamber for the
non-peptide ligand.
Second, antechamber tries to figure out things based on geometry. If there
are any bad contacts (for example) in the docked structure, that would be very
confusing to antechamber, which relies on having a good structure to work
from. That might be the cause of the specific problem you see (hard to tell
without more info.)
...dac
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Received on Sun May 31 2009 - 01:09:07 PDT
