VMD-L Mailing List

From: Nuno R. L. Ferreira (nunolf_at_ci.uc.pt)
Date: Mon Feb 27 2006 - 09:25:57 CST

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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