From: Gerald Quon (gtquon_at_student.cs.uwaterloo.ca)
Date: Mon Feb 09 2004 - 12:09:29 CST
Hi,
I'm a new user and am interested in using NAMD for minimization purposes.
I've downloaded the CHARMM potentials, and tried the following
minimization script, but it does not
seem to minimize my structures very well (when minimizing test native
PDB files, I get structures that are 5-6 angstroms off).
I was wondering if anyone could provide me with a 'standard' minimization
script that I could start off with, or give me suggestions on how to
improve mine? Thanks!
- Gerald Quon
University of Waterloo
Waterloo, Ontario, Canada
------------------------
# NAMD configuration file for PROT
# molecular system
structure 0.psf
# force field
paratypecharmm on
parameters par_all22_prot.inp
exclude scaled1-4
1-4scaling 1.0
# approximations
switching on
switchdist 8
cutoff 12
pairlistdist 13.5
margin 0
stepspercycle 20
#integrator
numsteps 10000
timestep 1
#output
outputenergies 1
outputtiming 100
binaryoutput no
imdon yes
imdfreq 1
imdport 3111
# molecular system
coordinates 0.pdb
#output
outputname 0_out
#dcdfreq 1000
# constraints/Fixed
fixedAtoms on
fixedAtomsFile 0.pdb
fixedAtomsCol B
#protocol
temperature 400
langevin no
rescaleFreq 50
rescaleTemp 400
#script
minimize 400
run 20000
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:38:24 CST