VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Wed Nov 23 2005 - 13:43:35 CST

VMD currently ignores CONNECT records in pdb files. If you just load
the pdb, VMD makes bonds based (in part?) on distance so it is not
surprising that it doesn't place this bond.

The way around that is to make a psf file using psfgen. You will have
to make a patch to create the disulfide bond (see PRES DISU in the
topology file and also the psfgen manual).

Psfgen manual: http://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/ug.pdf

On Nov 22, 2005, at 7:03 AM, andrea spitaleri wrote:

> Hi all,
> I have a file.pdb with CONECT flag at the end giving the S-S
> connection atom numbers. While in pymol or insight I can see the S-S
> bond,
> in vmd it doesn't appear at all. I am wondering if it is a problem of
> cutoff since the dist is quite large (0.25nm).
> Any help??
>
> Regards,
> Andrea
> --
> -------------------------------
> Andrea Spitaleri
> Dulbecco Telethon Institute
> c/o DIBIT Scientific Institute
> Biomolecular NMR, 1B4
> Via Olgettina 58
> 20132 Milano (Italy)
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