AMBER Archive (2009)

Subject: Re: [AMBER] Load protein complex to Xleap (Combine)

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Sun Mar 29 2009 - 13:41:13 CDT

On Sun, Mar 29, 2009, Rilei Yu wrote:
>  
> When I obtained the protein complex which was produced by docking a
> small peptide into a receptor, I wanted to perform the MD on this
> complex. But when I load the complex into the xleap, I found there are
> some errors on the ligand.

> a = loadpdb procomplex.pdb
> edit a
> # I found some errors on this small peptide.

What are these errors? Why can't they be fixed by editing the
"procomplex.pdb" files? If sybyl is making peptide ligands that Amber
cannot recognize, then you probably just need to edit the sybyl output
pdb files so that Amber *will* treat the ligand as a peptide.

As I suggested before, you will want to avoid using antechamber in this
situation.

...dac

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