VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Sat Feb 23 2008 - 17:29:35 CST

On Fri, 22 Feb 2008, fouchni_at_uni-osnabrueck.de wrote:

FO> Dear all,

dear F.

please note that re-posting a question to a mailing list rarely
increases the chance to get a useful answer. re-sending it to
individuals is even more annoying and increases the changes
of simply getting ignored. usually, if you do not get the
response that you were hoping for, or no response at all, then
it is most likely, that you have not asked the right question.

FO> I would like to replace a natural amino acid in PDB files with an
FO> unnatural one (spin label residue). I have a PDB file of spin label
FO> residue and its topology file from GROMACS and insightII. How can I add
FO> this information in the VMD?

please explain what exactly it is you are looking for and what
you plan to do with it. your information is not very extensive
and if you used GROMACS and Insight, why not use those tools
to do what you need to begin with?

if you want to replace a part of a PDB file with some other PDB file,
in most cases all you need would be a text editor.

VMD has a mutator plugin to perform single residue mutattions,
but that is targeted for simulations with NAMD using CHARMM
forcefields.

cheers,
   axel.

FO>
FO> Thanks in advance.
FO>
FO> With my best regards,
FO> F. Ouchni
FO>
FO> 

-- 
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Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
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If you make something idiot-proof, the universe creates a better idiot.