Re: The correct topology/parameter file and pgn

From: S.K. Ghosh (
Date: Tue Jun 03 2008 - 18:15:44 CDT

Hi Peter,

Thanks very much.

This psfgen is giving errors because the pdb file is for
streptavidin-biotin and the topology file is only for protein. So I need
CHARMM topology and parameter files for Biotin. Could someone help me with
suggestions where I could find these.

Thanks very much.


On Jun 3 2008, Peter Freddolino wrote:

>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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