VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sat Dec 19 2009 - 01:52:07 CST

Hi,
  I briefly read the PDB file you included in your note,
and it looked to me like you don't have it formatted into the
correct columns. Check the formatting of your PDB vs. the
PDB file format spec at www.rcsb.org and make sure you've got the fields
starting in the right columns.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Dec 17, 2009 at 03:24:58AM -0200, Ranyere Deyler 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:
>
> 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 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078