[gmx-users]build topology file for a molecule define with new residues

[Tsjerk Wassenaar]

Hi Justin (and Geraldine),

I think that cross-referring people asking about building topologies
to the exotic species wiki page by default is a bit too much. It's
Parameterization they need to read (and chapter 5 of the manual).
Exotic species are those weird atoms you sometimes encounter in
ligands/proteins (e.g. Ruthenium). Especially those darned transition
metals. But that doesn't apply to heparin, nor any of to the compounds
asked for lately on the list. Of course people have to be cautioned,
but the help should stick to the facts the question applies to.

O, and heparin has been simulated before. Geraldine, have you already
searched the archive/web/literature? Did you have a force field in
mind? The Prodrg server is a very bad idea (sorry Daan). Just had a
quick look for glucose, and compared the charges with the Gromos 45a3
ones, which have been parameterized with care. Almost scary.

Cheers,

Tsjerk

On Thu, Feb 21, 2008 at 5:34 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> Quoting cilpa at users.csc.fi:
>
>  > hi all,
>  > i would like make MD simulation of heparin. the only files i have is the
>  > pdb file from protein data bank but residues in this file are unknown by
>  > gromacs. so i have to build the topology file. Is anyone had ever built
>  > topology files and parameters files [or have any ideas] and could help in
>  > telling me the main steps to create those files?
>
>  Parameterization questions are asked almost daily.  Check the archive for such
>  inquiries about drugs, ligands, etc.  (I just replied to one this morning, as a
>  matter of fact).  Standard reading for such problems:
>
>  http://wiki.gromacs.org/index.php/Parameterization
>
>  http://wiki.gromacs.org/index.php/Exotic_Species
>
>  The PRODRG server can be used to generate primitive GROMOS topologies, but be
>  advised that the charges given in these topologies are often unsatisfactory.
>
>  -Justin
>
>
>  > geraldine cilpa
>  > Helsinki university
>  >
>  >
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>
>
>  ========================================
>
>  Justin A. Lemkul
>  Graduate Research Assistant
>  Department of Biochemistry
>  Virginia Tech
>  Blacksburg, VA
>  jalemkul at vt.edu | (540) 231-9080
>  http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
>  ========================================
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623