VMD-L Mailing List

From: Molybdos Kirkimpolakis (supercomputer.simulation_at_gmail.com)
Date: Mon Oct 17 2011 - 00:11:05 CDT

Thanks so much Dr Axel Kohlmeyer. This is working very well.

2011/10/15 Axel Kohlmeyer <akohlmey_at_gmail.com>

> 2011/10/15 Molybdos Kirkimpolakis <supercomputer.simulation_at_gmail.com>:
> > Dear VMD Masters,
> >
> > I want to select many groups of atoms, labelled only in one variable. I
> am
> > doing the following but I got an error.
> >
> > set sel [atomselect top "resid 743 to 748" or "resid 775 to 784" or
> "resid
> > 800 to 884" ]
>
> this is using wrong syntax. there must be only one argument (a single
> string)
> after 'top'.
>
> more likely you want:
>
> set sel [atomselect top "(resid 743 to 748) or (resid 775 to 784) or
> (resid 800 to 884)" ]
>
> > In addition I want to add a macro for my ions Na and Cl since I am using
> > amber forcefield they are named Na+ and Cl- in the pdb.
> >
> > When ever I try to do the following I got an error because vmd cannot
> parse
> > the + and - in the names
> >
> > atomselect delmacro ions
> > atomselect macro ions {resname Na+ Cl-}
>
> have you tried this?
>
> atomselect macro ions {resname 'Na+' 'Cl-'}
>
> > I believe there should be a way to overcome this problem. I will highly
> > appreciate your help in this matter.
>
> cheers,
> axel.
>
> >
> > Thanks
> >
> > --
> > cheers
> >
> > Molybdos Kirkimpolakis
> >
> > Πανεπιστήμιο Πατρών
> >
> > ΤΜΗΜΑ ΒΙΟΛΟΓΙΑΣ
> >
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
> 

-- 
cheers
Molybdos Kirkimpolakis
Πανεπιστήμιο Πατρών <http://www.biology.upatras.gr>
ΤΜΗΜΑ ΒΙΟΛΟΓΙΑΣ