topology file for compound

From: Yanlong Xu (yxu3_at_paws.lsu.edu)
Date: Mon Jul 26 2004 - 12:15:28 CDT

Hey, Dear NAMD users:
  I have one question and wish somebody know the answer and would like to share the solution here:
Is there any easier way to build a topology file for a small compound? I found a website http://xplor.csb.yale.edu/xplor/hetero that gives lots hetor groups xplor format topology file, but I had trouble to read them into psfgen and combine it with my protein PSF file. Anybody used that website before?
  Last, if somebody happen to have FAD topology file, that will be super great if you'd like to share it. :-)
  Or, maybe there is other better resource that we can look up and download the file? Thanks
Sincerely yours
Yanlong

----- Original Message -----
From: Brian Bennion <brian_at_youkai.llnl.gov>
Date: Wed, 21 Jul 2004 16:23:41 -0700 (PDT)
To: Ken Sale <sale_at_magnet.fsu.edu>
Subject: Re: namd-l: psfgen

>
> Hi Ken,
>
> You can use psfgen this way, but it still requires that at least 3 atoms
> in each residue have some coordinates so it can guess the rest. If no
> coordinates are given psfgen will choke, based on my past experience...
>
>
> On
> Wed, 21 Jul 2004, Ken Sale wrote:
>
> > Is there a way to use psfgen to add missing residues to a protein structure?
> > I am trying to add 3 missing N-term residues to a protein. I suppose I could
> > add an atom for each residue to the PDB with no coordinates and let psfgen
> > guess them, but I am hoping there is an easier way like simply providing the
> > sequence.
> >
> > Thanks,
> >
> > Ken
> >
>
> *****************************************************************
> **Brian Bennion, Ph.D. **
> **Computational and Systems Biology Division **
> **Biology and Biotechnology Research Program **
> **Lawrence Livermore National Laboratory **
> **P.O. Box 808, L-448 bennion1_at_llnl.gov **
> **7000 East Avenue phone: (925) 422-5722 **
> **Livermore, CA 94550 fax: (925) 424-6605 **
> *****************************************************************
>

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