Dear sir,
we have 1000
structures for a penta peptide.
we want to minimize all these structures using sander
program. But the petide has the uncharged terminal
residus. that is
NH2-TYR-GLY-GLY-PHE-MET-OH.
the problem is i can't run tleap.
because tehere is no parm file for ucharged amino
acids
in the amber library. In the amber library has the
dats
only for charged amino acids and standard amino acids.
so, could you please guide us how to minimize our
structers? or please send us any sample input file.
we have the problem only in the terminal residues.
after the minimization we want to calculte the rms
values to each structures with respect to first
structure. If you have any script for this
, please send us it.
we are using SGI(IRIX version 6) machine for this.
waiting for your reply.
yours sincerely
K.Vengadesan
=====
K. Vengadesan
Research Fellow,
Department of Crystallography and Biophysics
University of Madras
Guindy Campus, Chennai-600 025, INDIA
e-mail:venk11_at_yahoo.com
phone: 91 44 2351367
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Received on Sat Apr 21 2001 - 19:57:24 PDT
