Re: minimization of a cyclic peptide with NAMD

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Mon Sep 04 2006 - 16:20:42 CDT

You need to do that in psfgen when you create the structure. First build
the segment with "first none" and "last none", then apply the LINK patch
(and regenerate angles dihedrals) to join the two ends.

-Jim

On Mon, 4 Sep 2006, Idit Buch wrote:

> 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
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:42:33 CST