VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Oct 15 2011 - 17:33:49 CDT

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.