attached is the error list form the leap.log. The difference is in 1 atom, however, I don't it seems as if AMBER has added some atoms- possibly hydrogens.
________________________________
From: Dean Cuebas <deancuebas.missouristate.edu>
To: Chris Chris <alpharecept.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Wednesday, May 9, 2012 11:40 AM
Subject: Re: [AMBER] Problems doing MD on protein complex
Dear Chris
First, find out why the ligand in the complex has a differing # of atoms
than the ligand does in the file that contains only the ligand.
Dean
On 5/9/12 10:29 AM, "Chris Chris" <alpharecept.yahoo.com> wrote:
> I think the problem is with the small-molecule ligand (CTZ) in binding
>pocket of the protein complex I'm trying to use.
>
>Originally, there were too many bonds to each atom in the CTZ molecule. I
>used the SMILE software followed by REDS to get the right bond lengths
>and thus make it so each atom had the proper bond lengths and
>corrersponding # of Bonds (pdb file attached: (CTZ05.pdb). I then used
>antechamber to make the param and crd files. I followed the antechamber
>amber tutorial for this.
>
>The problem now appears to be the complex. The CTZ molecule in the
>binding pocket has too many bonds to it and this is probably causing the
>problem (attached pdb 2psj_ctz_compex...pdb). I originally got the
>complex from a molgro file in the mol2 format.
>
>I can't put the protein/ligand complex through SMILES again.
>
>How can I fix this problem so that the ligand in the complex doesn't have
>the bonding problem?
>
>Thanks,
>Chris
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- application/octet-stream attachment: leap.log
Received on Wed May 09 2012 - 15:00:01 PDT
