The correct topology/parameter file and pgn

From: S.K. Ghosh (
Date: Mon Jun 02 2008 - 15:55:06 CDT

Dear NAMD Users,

I am a newbie in NAMD simulations. Could you please suggest which
parameter/topology file should ideally be used for a simulation of
biotin-streptavidin in water, where I am using 1swe.pdb (streptavidin
complex with biotin).

Are the topology and parameter files used in the NAMD tutorial examples
(par_all27_prot_lipid.inp and top_all27_prot_lipid.inp) same as
par_all27_prot_lipid.rtf and top_all27_prot_lipid.rtf on Dr Mackerell's

Also, the pdb files available from RCSB Protein Databank do not contain H
atoms. So I do not need to remove the H atoms, as is done in the tutorial
for ubbiquitin. Could you please confirm this.

Finally, to create the psf file and NAMD compatible pdb file (with H) for
biotin-streptavidin, is it OK if I run the following .pgn file.

package require psfgen
topology top all27 prot lipid.inp
pdbalias residue HIS HSE
pdbalias atom ILE CD1 CD
segment BS {pdb 1swe.pdb} coordpdb 1swe.pdb BS
writepdb bs.pdb
writepsf bs.psf

Your suggestions will be immensely helpful.

Thanks very much.


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