Re: [AMBER] Problems doing MD on protein complex

From: Chris Chris <alpharecept.yahoo.com>
Date: Wed, 9 May 2012 14:58:45 -0700 (PDT)

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 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

Received on Wed May 09 2012 - 15:00:01 PDT
Custom Search