VMD-L Mailing List

From: Baker, Joseph (bakerj_at_tcnj.edu)
Date: Fri Sep 08 2023 - 07:15:42 CDT

Hi all,

Using the AmberTools program parmed one can create a version of a prmtop
file which contains chain label information. However, VMD does not seem to
import the information from that section of the modified prmtop file. The
section that gets added to the prmtop file is tagged as %FLAG
RESIDUE_CHAINID. Is it possible VMD is reading this information and storing
it in some variable when it reads the prmtop file and I could somehow
access it through the TKConsole, even though VMD is not using it to assign
chain labels to the residues? Or does VMD just not currently read that
section of the prmtop since it is not found in the "default" prmtop file
produced by tleap?

Thanks!
Joe

------
Joseph Baker, PhD
Associate Professor
Department of Chemistry
C212 Science Complex
The College of New Jersey
Ewing, NJ 08628
Phone: (609) 771-3173
Web: https://urldefense.com/v3/__http://www.bakercompchemlab.com__;!!DZ3fjg!74dtXtsgOyjjihP83D0ZiFhHi4d23R3pwKyHEkQCUbtlilzPs9ykqsUeGyjRlkZeJEXZNkRkdoejDFC-OQ$
Pronouns: he/him/his

Chair (2023), Trenton Local Section of the ACS
Chemistry Division Councilor (2021-2024), The Council on Undergraduate
Research