VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Apr 05 2006 - 23:14:27 CDT

Hi,
  A correction, as my prevoius response is not accurate.
Actually, these messages are not errors (psfgen messages that
begin with "Info" should be harmless). Given that they are the "info"
form of this message, they indicate that psfgen is correctly handling
the terminal residues. (which don't have a previous, or following residue,
which is why those impropers, bonds, etc are listed as "skipped").

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Apr 05, 2006 at 09:47:21PM -0500, John Stone wrote:
> Hi,
> You'll want to check your PDB file atom and segment IDs, see these
> related discussions on the NAMD-L list:
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/1454.html
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Apr 03, 2006 at 05:16:01PM +0900, Taeho Kim wrote:
> > Dear, all.
> >
> >
> > When I made a segment to make a .psf file, I met a error like below.
> >
> > ================================
> > vmd > segment NE {
> > ? first NONE
> > ? last NONE
> > ? pdb neurospora1.pdb
> > ? }
> > building segment NE
> > setting patch for first residue to NONE
> > setting patch for last residue to NONE
> > reading residues from pdb file neurospora1.pdb
> > extracted 283 residues from pdb file
> > Info: generating structure...
> > Info: skipping improper N-C-CA-HN at beginning of segment.
> > Info: skipping conformation C-N-CA-C at beginning of segment.
> > Info: skipping conformation C-CA-N-HN at beginning of segment.
> > Info: skipping bond C-N at end of segment.
> > Info: skipping improper C-CA-N-O at end of segment.
> > Info: skipping conformation CA-C-N-CA at end of segment.
> > Info: skipping conformation N-CA-C-O at end of segment.
> > Info: skipping conformation N-CA-C-N at end of segment.
> > Info: segment complete.
> > =================================
> >
> > Please let me know the reason or solvation.
> >
> > Thank you very much in advance.
> >
> > =====
> > Taeho Kim(±èÅÂÈ£)
> --
> 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 

-- 
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