Re: The correct topology/parameter file and pgn

From: Peter Freddolino (
Date: Tue Jun 03 2008 - 15:11:55 CDT

Hi Sourav,
the parameters from the namd tutorial should be the same as the ones you
mention from MacKerell's website; you can always use diff or a similar
tool to confirm this.

In your psfgen input script, you appear to be missing the underscores in
the topology file name. Also, segment NAME {pdb blah} and coordpdb blah
NAME are separate statements and thus should go on separate lines. You
will also need to modify that psfgen script if you have anything unusual
in your protein (disulfide bonds, etc.). It's best to look at the
structure after running psfgen to verify that it appears chemically correct.


S.K. Ghosh wrote:
> 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 website?
> 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
> guesscoord
> writepdb bs.pdb
> writepsf bs.psf
> Your suggestions will be immensely helpful.
> Thanks very much.
> Sourav

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