VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Apr 13 2006 - 01:34:09 CDT

Nuno and other Gromacs users,
  I wanted to let you know that the new builds recognize the O1 and O2
Gromacs terminal atom names automatically now. Going forward VMD is going
to have to have a better system for getting this information from file
reader plugins or to re-analyze the structure on the fly as it's probably
a hopeless pursuit to endlessly teach it the atom naming quirks of all
of the different packages. I'm happy to do it for simple non-conflicting
cases like this in the short term though, so if you know of others, please
send me an email.

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Feb 27, 2006 at 03:25:57PM -0000, Nuno R. L. Ferreira wrote:
> Hi *
>
> Well, I'm going to answer my question, after having talked with a colleague
> of mine, J.Rui.
>
> The pdb that caused that warning, was produced by Gromacs, where the Cter is
> charged (-1), pH7.
> The carboxylic terminus of proteins have the following atoms when using
> Gromos like forcefields:
>
> --> if Cter is charged (-1): C O1 O2
> --> if Cter is not charged : C O OT HO
>
> Vmd recognizes protein residues, when there's atoms named C, N, CA, and O in
> the same resid.
> Vmd also recognizes OT1 and OT2. So there's no problems if the the .gro has
> a Cter not charged!
>
> But in my case, I have a O1 and O2, no O atom. That's why Vmd complains.
> When I change the O1 Cterminal atom on the gromacs .gro file to O, VMD stops
> to give the warning, and if I issue:
>
> set sel [atomselect top "protein name CA"]
> $sel num
>
> I get *26* out of 26 residues.
>
> So, probably O1 O2 should also be added to that list of atoms recognized by
> VMD, since these are default names on the forcefield.
>
> Best regards,
> Nuno
>
>
> ----- Original Message -----
> From: "Nuno R. L. Ferreira" <nunolf_at_ci.uc.pt>
> To: "vmd mailing list" <vmd-l_at_ks.uiuc.edu>
> Sent: Saturday, February 25, 2006 5:42 PM
> Subject: vmd-l: Warning) Unusual bond between residues 25 and 26
>
>
> > Hi *
> >
> > When I load a peptide of *26* residues, I get the following warning:
> > Warning) Unusual bond between residues 25 and 26
> >
> > In the manual it is said that for terminal aminoacids this could happen.
> >
> > If I do the following:
> >
> > set sel [atomselect top "protein name CA"]
> > $sel num
> >
> > I get *25*
> > Any operation done on that $sel, will not describe my entire peptide. The
> > "protein" word, is not recognizing the 26th a.a.
> >
> > But, the info messages on the vmd console, tell me that:
> > Info) Residues: 26
> >
> > How can I surpass this?
> > BTW, is there a command to calculate the number of residues on the loaded
> > frame? I can´t find it on the manual.
> >
> > Best regards,
> > Nuno
> >
> > ######################################
> > Nuno Ricardo Santos Loureiro da Silva Ferreira
> > Departamento de Química
> > Faculdade de Ciências e Tecnologia
> > Universidade de Coimbra
> > 3004-535 Coimbra - Portugal
> > Fax: +351 239 827703 - www.biolchem.qui.uc.pt
> > ########################################
> >
> >
> >
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NIH Resource for Macromolecular Modeling and Bioinformatics
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