Re: Problem generating psf file in psfgen

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Dec 17 2009 - 01:38:00 CST

On Thu, Dec 17, 2009 at 12:20 AM, Ranyere Deyler <ranyere_at_gmail.com> wrote:
> Dear all, i've recently started working with namd and i'm with a big problem
> in generating a psf  file from a pdb file. The pdb file is very simple, it's
> just columns of athoms and they're fixed. There's no bond or anything, i
> suposed it would be very easy to generate the psf in this conditions, but it
> doesn't seem so. Well, first i made a pgn file:

things don't work like this. you have to first understand how the
necessary information for running an MD is collected from CHARMM
style input files. for example, psfgen processes input data based on
residues and compares them to a topology database. for the kind of
system it would be easier to generate the parameter file manually and
you don't need psfgen, just load the .pdb and save it again as .psf
(after deleting all bonds).

please note that the whole build and usage process and the corresponding
tutorials and documentation for NAMD assume that you are working on
biomolecules, i.e. take a crystal structure from the PDB and then want to
set up a simulation for that.

cheers,
   axel.

>
> package require psfgen
> topology top_all27_prot_lipid.inp
> segment U {pdb coord_helio.pdb}
> coordpdb coord_helio.pdb U
> writepdb helio.pdb
> writepsf helio.psf
>
> But i got the error message:
>
> building segment U
> reading residues from pdb file small_helio.pdb
> unknown residue type
> extracted 1 residues from pdb file
> Info: generating structure...
> unknown residue type
>
> I tryed removing the line "segment...." but it gives another error message:
> "no segment".
>
> And the pdb file is below, it's a short version of my structure, smaller
> columns. Well, i think the problem could be on the segment, because i'm not
> very sure that i'm doing it write, but i tried without it and got error. So,
> if anyone could tell me what i'm doing wrong i would appreciate. Thanks a
> lot.
>
>
> CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
>
> ATOM 1 HE X 1 0.000 0.000 0.000 1.00 0.00 HE
>
> ATOM 2 HE X 1 0.000 0.000 2.000 1.00 0.00 HE
>
> ATOM 3 HE X 1 0.000 0.000 4.000 1.00 0.00 HE
>
> ATOM 4 HE X 1 0.000 0.000 6.000 1.00 0.00 HE
>
> ATOM 5 HE X 1 5.000 0.000 0.000 1.00 0.00 HE
>
> ATOM 6 HE X 1 5.000 0.000 2.000 1.00 0.00 HE
>
> ATOM 7 HE X 1 5.000 0.000 4.000 1.00 0.00 HE
>
> ATOM 8 HE X 1 5.000 0.000 6.000 1.00 0.00 HE
>
> ATOM 9 HE X 1 0.000 5.000 0.000 1.00 0.00 HE
>
> ATOM 10 HE X 1 0.000 5.000 2.000 1.00 0.00 HE
>
> ATOM 11 HE X 1 0.000 5.000 4.000 1.00 0.00 HE
>
> ATOM 12 HE X 1 0.000 5.000 6.000 1.00 0.00 HE
>
> ATOM 13 HE X 1 5.000 5.000 0.000 1.00 0.00 HE
>
> ATOM 14 HE X 1 5.000 5.000 2.000 1.00 0.00 HE
>
> ATOM 15 HE X 1 5.000 5.000 4.000 1.00 0.00 HE
>
> ATOM 16 HE X 1 5.000 5.000 6.000 1.00 0.00 HE
>
> END

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.

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