From: Josh Vermaas (
Date: Mon Jun 21 2021 - 07:54:41 CDT

What was your topotools command? I'm betting the order of selections has
the water boxes coming first. Topotools will put the atoms in the order
of the selections, and residue numbering depends on atom order.


On 6/20/21 6:10 AM, Nagendra Prasad wrote:
> Dear VMD users,
> I have tried to access the individual monomers in the membrane based
> on the residues and resids but could not access them. I have added
> water boxes below and above the membrane and used topotools to merge
> and generate psf pdbs for the system, and surprisingly topo tools have
> changed the residue and resids of membrane and assigned single residue
> and resid for the whole membrane. I have tried to access them based on
> atom types and name and it only selects individual atoms but not the
> monomers. Please give me some suggestions to rectify this problem.
> Thanks in advance.
> Thanks & Regards
> G Nagendraprasad
> PhD IITGuwahati

Josh Vermaas
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University;!!DZ3fjg!rfJ2Mmw03MrHNOfYj4FvDcP6dpTUjQQer_sDKoCsFTEVXCm80i_DtxTe7yx4isNdKw$