VMD-L Mailing List

From: Maryam (maryam.kowsar_at_gmail.com)
Date: Mon Jan 31 2022 - 13:17:01 CST

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> 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
> Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
> Michigan State Universityhttps://prl.natsci.msu.edu/people/faculty/josh-vermaas/
>
>