how to minimize the energy of a protein using CHARMM FF in NAMD

From: Kalyan chaitanya (kalyanpulipaka_at_gmail.com)
Date: Thu Feb 07 2008 - 09:29:08 CST

Dear all,

I want to minimize a protein using charmm force field, i have a specific
input file (see attachment) using which i want to do this, i have been using
a standard procedure in vegaz (*namd2 file.namd > file.out*) and using a
standard parameter file (see attachment). Can any one tell me how to proceed
with minimization of a protein using the specific input file.

I hope I made my question clear, in case any one doesn't understand my
question, please let me know.

Regards,

Kalyan.


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