VMD-L Mailing List

From: Vermaas, Josh (vermaasj_at_msu.edu)
Date: Mon Jan 31 2022 - 14:52:57 CST

What I’d suggest is to figure out what atomselection captures what you want just by looking in VMD. The “protein” macro makes some CHARMM-specific assumptions, so if you are using a different force field, you might need to be more creative in defining an atomselection that picks out your whole protein. Playing with it visually before going into the script would be what I recommend.

-Josh

From: Maryam <maryam.kowsar_at_gmail.com>
Date: Monday, January 31, 2022 at 2:17 PM
To: "Vermaas, Josh" <vermaasj_at_msu.edu>
Cc: VMD Mailing List <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: Protein-ligand interactions

Hi Josh and Harper

Thank you for your response.
I tried a bunch of selections and the only successful one was "resid 283" "resid 1709" for which 283 is from the protein and 1709 is the ligand. I want to scan the whole protein but "protein" does not seem to work. Any suggestions on how to do that?

Thanks

On Mon, Jan 31, 2022 at 12:43 PM Josh Vermaas <vermaasj_at_msu.edu<mailto:vermaasj_at_msu.edu>> wrote:
What is your selection for protein? I think contactFreq needs two arguments, one that is atomselection text that picks out protein, and another text that picks out the ligand. "Selection for protein" is not valid atomselection text.

-Josh
On 1/31/22 11:39 AM, Maryam wrote:
Hello

I'd like to find the number of close contacts and contact areas for a receptor-ligand interactions. I use the
source ContactFreq.tcl
in the TkConsole and then run
contactFreq "selection for protein" "selection for ligand"
but it gives me this error
atomselect: cannot parse selection text: selection for protein and noh and within 4 of (selection for ligand and noh)
Is there a point I am missing?
Your help is appreciated.

Thanks 

--
Josh Vermaas
vermaasj_at_msu.edu<mailto:vermaasj_at_msu.edu>
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University
https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!oPwTBYEvwaCGKBsyyEfGD4y8ruaeAufPLzXVcLB0Xxx1oxIiCbHOwRzOneEx-yGylw$