minimization of a cyclic peptide with NAMD

From: Idit Buch (
Date: Mon Sep 04 2006 - 04:22:03 CDT


I have a cyclic peptide which I'm trying to minimize with NAMD. The problem
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
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


Idit Buch

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:42:32 CST