VMD-L Mailing List

From: Akash Pandya (akashpandya93_at_gmail.com)
Date: Thu Apr 16 2020 - 09:22:00 CDT

Thank you for your response/suggestion. I'm not interested in calculating
minimum distance. I just simply want to obtain the number of ligand
molecules within 5 A of each residue. Currently, I have an output file with
frame number and number of molecules. I want the output to have number of
molecules for each of the 442 residues for each time frame, if that makes
sense. So from my script, do you have any suggestions on how I can achieve
this?

Many thanks,
Akash

On Thu, Apr 16, 2020 at 2:24 PM Adupa Vasista <adupavasista_at_gmail.com>
wrote:

> 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.*
>