VMD-L Mailing List

From: Adupa Vasista (adupavasista_at_gmail.com)
Date: Thu Apr 16 2020 - 08:24:27 CDT

Dear Akash, It is similar to finding contacts of a ligand with a protein.
Then, I suggest you use this script
https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/att-5681/newcontacts.tcl

Thank you.

On Thu, Apr 16, 2020 at 6:18 PM Akash Pandya <akashpandya93_at_gmail.com>
wrote:

> Hi,
>
> I am new to the VMD mailing list. I want to count the number of ligand
> molecules within 5 A around my protein. So I wrote a tcl script for this
> (shown below):
>
> set frames [molinfo top get numframes]
> set fp [open "LIG.txt" w]
> set protein "resid 1 to 442"
> for {set i 0} {$i < $frames} {incr i} {
> puts "Frame: $i"
> set a [atomselect top "(index 6616 to 8155 and same index
> as within 5 of ($protein))" frame $i]
> set num [$a num]
> puts $fp "$i $num"
> $a delete
> }
> close $fp
>
> index 6616 to 8155 is my ligand. This script gives the number of ligand
> molecules at each time frame. So my question is what command can I enter to
> also get the number of ligand molecules around EACH RESIDUE (resid 1 to
> 442)?
>
> Cheers,
> Akash
>
> 

-- 
*A.VasistaM.Tech,Department Of Chemical Engineering,*
*IIT Guwahati.*