VMD-L Mailing List

From: Davit Hakobyan (davhak2000_at_hotmail.com)
Date: Thu May 06 2004 - 01:05:11 CDT

Hi Tim,

Thank you very much for you advice. I will look at MOE and might follow your
advice and ask at namd-l about parameter development.

Regards,
Davit.

>From: Tim Isgro <timisgro_at_ks.uiuc.edu>
>To: Davit Hakobyan <davhak2000_at_hotmail.com>
>CC: vmd-l_at_ks.uiuc.edu
>Subject: Re: vmd-l: Include HETATM into *.psf file
>Date: Wed, 5 May 2004 17:24:12 -0500 (CDT)
>
>Hi Davit,
>If you want to run simulations with the substrate, you will need to
>develop parameters for it (as well as a topology file entry for it). The
>program MOE can perform a parameter file search and will give parameters
>and atomic charges based on similarities between atoms in your molecule
>and those already defined in the Charm parameter files. (If you want to
>know more, parameter development is probably a discussion more suited
>toward the namd-l list.)
>Tim
>
>
>On Mon, 3 May 2004, Davit Hakobyan wrote:
>
> > Hi All,
> >
> > I have a pdb file of an enzyme (phosphoglycerate mutase) which is
>complexed
> > with its substrate (3-phosphoglycerate with HETATM record). As the
>substrate
> > is not a valid residue (with name 3PG, which is not a name of any valid
> > residue) it is rejected by topology file when I try to generate a new
>*.pdb
> > file which will contain hydrogen atoms in addition (or a *.psf file).
> >
> > Is there a way to include substrate (HETATM records) in further
>simulation
> > along with the protein (ATOM records) itself ?
> >
> > Thanks for any help.
> >
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