VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Mar 26 2008 - 23:19:40 CDT

On Thu, 27 Mar 2008, Ben Chern wrote:

BC> Hello,
BC> as we know, the interactions between different part is the reason of the
BC> protein conformation.
BC> Then can VMD detect and show the interactions that is reponsible for the
BC> protein conformation in every scale(primary, secondary, tertiary and
BC> quarternary structure)?

of course not. VMD is a _visualization_ program. it only shows
information that you feed it. the interactions itself have to
be modeled with some method (forcefield, quantum chemistry etc.).

those are a complex interplay of multiple types of interactions
(short range and long range) and "volume" and/or entropy. if you
could disentangle it that easily there would be no reason for
projects like folding_at_home and so on...

cheers,
   axel. 

-- 
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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.