Mailinglist Archive: opensuse (4547 mails)

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Re: [SLE] Protein Folding source code
  • From: Luca Mollica <luca_mollica@xxxxxxxxxxx>
  • Date: Wed, 5 May 2004 18:02:14 +0200
  • Message-id: <200405051802.14656.luca_mollica@xxxxxxxxxxx>
On Wednesday 05 May 2004 16:49, Martin Mielke wrote:
> Hi again,
> replying to myself? no :P
> I just want to add something on this subject: can this software (GROMACS
> or whatever) be used to calculate/simulate proteine torsion/flexibility?

GROMACS is a very powerful tool, but it does not do everything auomatically:
very often in order to compute some parameters you have to use the options
flag for each command and/or modify the index files (the files that contain
parts of the system defined through atomic poition and topologies).
For example, Phi/Psi angles are not computed automatically for each residue,
but I have managed to compute them for a single residue setting up the index
file correctly and defining planes, dihedral and vectors accordingly
So, very often with GROMACS you have to work a lot in a tuning fashion in
order to compute quantities you are interested in.

Please browse GMX mailing list at the URL

and maybe you will find something about your query: this mailing list is very
active, and you wil find almost every answers to your questions.



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