VMD-L Mailing List

From: Arthur Pereira da Fonseca (arthurpfonseca3k_at_hotmail.com)
Date: Wed Aug 17 2022 - 10:21:48 CDT

Yes, I’m trying to select protein. But the atomselect $mol “protein” does not return the last residue, probably because vmd thinks it is a solvent. If I do $last_residue get protein I get 0, meaning that VMD dont see it as a protein.

So I created a macro to address this issue.

But it's still strange. I checked all my gromacs simulations and all of them are the same. The last residue from each chain is not a protein. Not even the selection “backbone” works on them. Even if they got the desired atoms. I think that is because of the patch used in the C-terminal. But would need further investigation, the macro will do it for now.

Thanks all

De: Josh Vermaas<mailto:vermaasj_at_msu.edu>
Enviado:quarta-feira, 17 de agosto de 2022 10:23
Para: Arthur Pereira da Fonseca<mailto:arthurpfonseca3k_at_hotmail.com>; vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>
Assunto: Re: vmd-l: Protein residue read as solvent

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<mailto:vermaasj_at_msu.edu>
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University
vermaaslab.github.io