VMD-L Mailing List

From: Josh Vermaas (vermaasj_at_msu.edu)
Date: Wed Aug 17 2022 - 08:23:19 CDT

What are you actually trying to do? If you want to select protein, the
"protein" macro is usually what I use. I am less familiar about what the
solvent macro does, since it isn't one of the default macros from the
user guide.

-Josh

On 8/16/22 7:49 PM, Arthur Pereira da Fonseca 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?
> 

-- 
Josh Vermaas
vermaasj_at_msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University
vermaaslab.github.io