VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Sep 15 2005 - 11:41:18 CDT

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
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