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

[cilpa at users.csc.fi]

HI Tsjerk,

Well i found i didn't find much in the litterature, some publications give
some informations about structures (angles, bonds, dihedrals) but it's
theoretical calculation using PM3 method. So i really don't know about how
to handle the problem of force field. I now need to get and gathered as
much informations possible. I had a look to this exotic species but indeed
this is another problem with no link with glycoaminoglycans molecules. but
they just mention to be careful about usage of force field , consistency
with the description of the all system under interest. So far i'm from
scratch.
thank you for advisise
geraldine

On Fri, February 22, 2008 10:52 am, Tsjerk Wassenaar wrote:
> 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
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