VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Dec 02 2005 - 13:07:24 CST

Andrea,
  I've got a new VMD build that merges in CONECT records with the
automatic distance-based bond search now. The new code will also let
you disable either of the PDB CONECT records or the automatic bond search
so you can override this behavior if you want. Let me know if you want to
try this new build, it's not posted on the web yet.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Nov 29, 2005 at 10:22:52AM +0100, andrea spitaleri wrote:
> Hi all,
> thanks for fixing this "issue". However, I have noticed another
> "problem". I have got a file.pdb and it is visualised properly. After
> feeding it to the gromcas tools (such as pdb2gmx or editconf ), the
> terminus aminoacid seems unbonded. In fact, if I select "protein", the
> terminus residue is not selected. That's strange since in gromacs
> topology file the C-N bond is still there. The bond distance is within
> the cutoff, I guess.
>
>
> Regards,
>
> andrea
>
> John Stone wrote:
>
> >Hi,
> > I think that doing what others suggested is the best thing in the short
> >term, but I wanted to mention that I now have CONECT record reading in the
> >VMD PDB reader, and I'm working on making it do the right thing since most
> >PDB files only have CONECT records for a small subset of the bonds in the
> >system (usually only the unusual ones). I've got a bit more work to do,
> >but
> >when it's done this will "just work", in the future.
> >
> > John
> >
> >On Tue, Nov 22, 2005 at 02:03:52PM +0100, 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)
> >>Get Firefox! <http://www.spreadfirefox.com/?q=affiliates&id=0&t=85>
> >>-------------------------------
> >>
> >>
> >
> >
> >
>
> --
> -------------------------------
> Andrea Spitaleri
> Dulbecco Telethon Institute
> c/o DIBIT Scientific Institute
> Biomolecular NMR, 1B4
> Via Olgettina 58
> 20132 Milano (Italy)
> Get Firefox! <http://www.spreadfirefox.com/?q=affiliates&id=0&t=85>
> ------------------------------- 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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