When I load the pdb file, the only warnings are that in the ligand there are some duplicate atoms. If I do "edit" on the file in xleap, the ligand is distorted with broken bonds.
John M. Beale, Jr.
John M. Beale, Jr., Ph.D.
Professor of Medicinal Chemistry and Pharmacognosy
Saint Louis College of Pharmacy
4588 Parkview Place
Saint Louis, Missouri 63110-1088
Office: 314-446-8461
Cell: 314-315-0409
FAX: 314-446-8460
John.Beale.stlcop.edu
-----Original Message-----
From: Bill Ross [mailto:ross.cgl.ucsf.edu]
Sent: Wednesday, April 13, 2016 2:42 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Antechamber Problem
Does it look ok in xleap? When the pdb loads, are there any warnings?
Bill
On 4/13/16 12:18 AM, Beale, John wrote:
> Good morning,
>
> I am using Amber 14 with AmberTools 15. I am trying to build a set of structures of an 88-residue peptide bound to a series of small molecule ligands. To build these molecules, I am trying to use Antechamber. I ran the Antechamber tutorial, and all of the steps worked as they were supposed to. To bind my own small molecule ligands, I use Antechamber to create frcmod and lib files. In xleap, I load the frcmod (loadAmberParams) and lib (loadoff) parameters, and then I try to load the peptide-ligand complex. The complex loads into xleap, but when I view it in VMD or Chimera, I find that the structure of the ligand has become distorted. Some of the intramolecular bonds have become very long, and some of the bonds are broken. The ligand is the only part of the complex that is faulty. The peptide is fine.
>
> Has anyone else encountered this problem? Is there a solution?
>
> Cheers!
>
> John Beale
>
> John M. Beale, Jr.
> John M. Beale, Jr., Ph.D.
> Professor of Medicinal Chemistry and Pharmacognosy Saint Louis College
> of Pharmacy
> 4588 Parkview Place
> Saint Louis, Missouri 63110-1088
> Office: 314-446-8461
> Cell: 314-315-0409
> FAX: 314-446-8460
> John.Beale.stlcop.edu<mailto:John.Beale.stlcop.edu>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed Apr 13 2016 - 01:00:05 PDT
