VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Sep 16 2005 - 11:17:13 CDT

Hi Sergio,
  It isn't done yet, but it's something I'm currently working on..
I'll let VMD-L know when I have a version available for you to test.

  John

On Thu, Sep 15, 2005 at 10:52:21PM -0400, Sergio Anis wrote:
> hi John,
>
> welcome back.
> does the new version load the pdb according to the conect records? from wich
> version? (i have 1.8.3)
>
> thanks,
> Sergio
>
> -------Original Message-------
>
> From: John Stone
> Date: 09/15/05 13:20:27
> To: Sergio Anis
> Cc: vmd-l_at_ks.uiuc.edu; Jen-Chang Chen
> Subject: Re: vmd-l: writing pdb
>
> Hi,
> I've just returned from a conference and am still catching up on emails...
> The PDB plugin used by all of the previous versions of VMD ignores the
> CONECT
> records, so the CONECT records aren't the cause of your specific problem.
> Most likely the issue is that you've got atoms clashing or structures with
> an unusual scale. When you load a PDB file without a PSF file, VMD uses a
> distance-based bond search, and so if you have an area with unusually high
> atom density, you can get error messages like these. If you build a proper
> structure with 'psfgen' and then load a matching PSF file into VMD, these
> errors will go away.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Sep 14, 2005 at 04:06:48AM -0700, Sergio Anis wrote:
> > i re-check the CONECT statements and found out some mistakes, there are
> some 'dangling' atoms. i guess that they are responsible for the error
> messages 'exceeded number of bonds' since the software is not able to tell
> if they belong to the protein or the heterogroup.
> >
> > thanks for your help
> > Sergio
> >
> > ----- Original Message -----
> > From: Dow Hurst DPHURST
> > Date: 09/13/05 16:16:12
> > To: Sergio Anis
> > Subject: Re: vmd-l: writing pdb
> >
> >
> >
> >
> >
> > Not necessarily, it depends on how the code is designed to interpret the
> > PDB file. If no connectivity information is included in the PDB file and
> > also if the program uses topology files as a reference, then you might not
> > see anything or just unconnected dots. PDB is great for well defined
> > proteins but can give problems with small molecules and so on.
> > Dow
> >
> >
>
> --
> 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