VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Mon Feb 18 2013 - 12:58:36 CST

Hi Jorgen,

The first one is simple:

(protein and not hydrogen) and same residue as within 7.5 of residue TIP

For the second issue, have you tried using double quotes? I know that
VMD's atomselection parser handles selections differently with double
quotes than it does without, and that using a selection like:

resname "Mg+"

might solve your problem.

-Josh Vermaas

On 02/18/2013 11:45 AM, Jorgen Simonsen wrote:
> Hi all,
>
> I am trying to make a selection per residue something like this
>
> (protein and not hydrogen) and within 7.5 of residue TIP
>
> I would like that the atoms return contain the whole amino acids right
> it gives me what I ask for - atoms within my cut off - it is possible
> to get the whole residue?
> Also I have some issues with selecting ions like this Na+, Mg+ (from
> amber) etc. When I try to get them with the atomselection like this
>
> resname Mg+ or resname Mg\+ it states unable to parse selection. How
> to include the "+"?
>
> Thanks