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From: Arthur Pereira da Fonseca (arthurpfonseca3k_at_hotmail.com)
Date: Tue Aug 16 2022 - 18:49:52 CDT

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?