VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Aug 17 2022 - 07:48:42 CDT

solvent is a predefined atomselect macro and you should be able modify it
with the "atomselect macro" command.

On Tue, Aug 16, 2022 at 8:33 PM Arthur Pereira da Fonseca <
arthurpfonseca3k_at_hotmail.com> wrote:

> Hello all,
>
>
>
> I've run a md simulation on gromacs and now I’m trying to open the results
> with vmd. My molecule has two protein chains and is solvated in water. When
> I try to open it with vmd, for some reason, it thinks that the last residue
> from each protein chain is actually a solvent. So I can’t select them using [atomselect
> $mol “not solvent”].
>
>
>
> Lets say I create a variable called last_residue with [atomselect $mol
> "resid index"].
>
>
>
> When I check $last_residue get resname, I get “SER” so everything is
> looking fine. But if I do $last_residue get solvent, I get 1 indicating
> that this is really interpreted as a solvent by vmd. Didn't find any
> difference in the molecule pdb file tho.
>
>
>
> I tried to run $last_residue set solvent 0, But it throws an error:
>
> atomsel object: set: data not modifiable: solvent
>
>
>
> So what can I do to make vmd read these residues as not solvents?
>
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!9uBLUu2Yc1vG11O2enQvjeh50Z038MiKYmJMNl7GuOscGM7B65Pcwl5-Mgvqa2wmtUq5cSj4K_NhlzUUlw$  
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.