From: Idit Buch (iditbuch_at_gmail.com)
Date: Mon Sep 04 2006 - 04:22:03 CDT
Hello,
I have a cyclic peptide which I'm trying to minimize with NAMD. The problem
is
that I don't know how to make NAMD consider a peptide bond between the
first and last residue. Right now the minimization process disconnects these
residues.
The NAMD parameter file is:
# Force Field
paratypecharmm on
parameters par_all22_prot.inp
exclude scaled1-4
1-4scaling 1.0
# Molecular System
coordinates nano_inp.pdb
structure nano_inp.psf
# approximations
switching on
switchdist 10
cutoff 12
pairlistdist 14.0
stepspercycle 20
margin 0
# protocol
seed 72134
rigidBonds none
timestep 1.0
fullElectFrequency 5
BerendsenPressure off
# output
DCDunitcell on
wrapall on
outputname minimiz
restartname mdminrst_bin
DCDfile minimiz.dcd
restartfreq 1000
outputenergies 500
outputtiming 1000
dcdfreq 2000
binaryoutput no
minimization on
numsteps 20000
Thanks
Idit Buch
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