VMD-L Mailing List

From: Justin Gullingsrud (justinrocks_at_gmail.com)
Date: Tue Oct 26 2004 - 18:46:21 CDT

Jeremy,

Don't worry; these are common problems. Your protein is a homodimer,
so you need to create at least two segments, one for each chain (and
probably a third for chain 'I'). Split the pdb file into separate
pieces, and enter a new segment statement and coordpdb statement for
each.

As for ABA, there is no residue definition, so you basically have two
choices: (1) design a new topology for it, or (2) pretend it's
something else, like a Ser. Sometimes you can use an existing residue
definition as a template.

Cheers,
Justin

On Tue, 26 Oct 2004 11:39:16 -0500, jin <jin_at_mail.ku.edu> wrote:
> hello,
> I am trying to generate the pdb and psf file for protein 4HVP, but I am
> getting errors using the psfgen command. I'll describe what I have done so
> far.
>
> 1)I downloaded the pdb file for 4HVP and loaded in VMD, and generated hvpp.pdb
> file for 4hvp without hydrogen bond.
> 2)I then try to create a psf file using a psfgen command on 'hvp.pgn' file I
> generated from the NAMD tutorial file. I also downloaded the topology file
> 'top_all27_prot_lipid.inp'.
>
> The script for hvp.pgn :
> package require psfgen
> topology top_all27_prot_lipid.inp
> alias residue HIS HSE
> alias atom ILE CD1 CD
> segment U {pdb hvpp.pdb}
> coordpdb hvpp.pdb U
> guesscoord
> writepdb hvp.pdb
> writepsf hvp.psf
>
> 3) when I type 'psfgen hvp.pgn', it gave me follow errors:
>
> unknown residue type ABA
> duplicate residue key PRO
> duplicate residue key IGN
>
> the list goes on with many duplicate residue keys and it ends saying the the
> molecule was destroyed bay Fatal error. Is there something I'm doing wrong?
> Please help, I appreciate it
>
> thank you,jeremy
>
> 

-- 
The spirit of Plato dies hard.  We have been unable to escape the
philosophical tradition that what we can see and measure in the world
is merely the superficial and imperfect representation of an
underlying reality.
                -- S.J. Gould, "The Mismeasure of Man"