peptide simulation

From: Matan Dishon (
Date: Mon Jun 27 2005 - 03:28:18 CDT

I am a new NAMD user, I have already done some short simulation to peptides
using NAMD just to get the hang of it, using the needed files ect.
 I have some questions before I dive deep into my project, which is
retrieving peptide 3D conformations when I have only the peptide sequence
and no other information.
 I would appreciate an experts opinion to some questions, so I don't waste
my time on an unattainable missions.
  1) I would like to know if it is possible to simulate (minimize energy)
 a peptide of 7 amino acid into a global minima without any nmr restraints
or other information except peptide sequence?
 Will I be able to retrieve the real (as in nature) peptide conformation in
a solvent (water)
 2) Is the use of simulated annealing enough to achieve this?
3) are there other or additional techniques I can use?
4) Is there a script (PSF file ) for simulated annealing?
5) Is there an information I can get in order to learn this subject (SA) in
the context of NAMD (how to write a SA script? what are the important
factors ect.?
6) Question number (1) regarding 12 amino acid long peptides (what is the
longest possible?)
 Thank you in advance
 Best regards,

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