VMD-L Mailing List

From: Akash Pandya (akashpandya93_at_gmail.com)
Date: Thu Apr 16 2020 - 10:27:16 CDT

I already know how to loop over the frames (as shown in my script) I want to know how I get number of molecules for individual residues rather than for the whole protein.

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

Sent from my iPhone

> On 16 Apr 2020, at 15:44, Adupa Vasista <adupavasista_at_gmail.com> wrote:
>
> 
> It will not calculate the minimum distance, but you need to give a minimum distance, in your case 5 A of the entire protein. But this script will not give you for each frame, rather it gives as a whole.
>
> Let's say you need to calculate the Number of Contacts between a chain of the protein and your ligand at distance criteria of 5 A for the entire simulation, then the command will be after sourcing the file: fResPair "protein and chain A" "ligand_resname" 5 $Firstframe $Lastframe.
>
> If you run a for loop for the frames, I guess you will get what you need.
>
> Thank you.
>
>> On Thu, Apr 16, 2020 at 7:51 PM Akash Pandya <akashpandya93_at_gmail.com> wrote:
>> Thank you for your response/suggestion. I'm not interested in calculating minimum distance. I just simply want to obtain the number of ligand molecules within 5 A of each residue. Currently, I have an output file with frame number and number of molecules. I want the output to have number of molecules for each of the 442 residues for each time frame, if that makes sense. So from my script, do you have any suggestions on how I can achieve this?
>>
>> Many thanks,
>> Akash
>>
>>> On Thu, Apr 16, 2020 at 2:24 PM Adupa Vasista <adupavasista_at_gmail.com> wrote:
>>> Dear Akash, It is similar to finding contacts of a ligand with a protein. Then, I suggest you use this script
>>> https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/att-5681/newcontacts.tcl
>>>
>>> Thank you.
>>>
>>>> On Thu, Apr 16, 2020 at 6:18 PM Akash Pandya <akashpandya93_at_gmail.com> wrote:
>>>> Hi,
>>>>
>>>> I am new to the VMD mailing list. I want to count the number of ligand molecules within 5 A around my protein. So I wrote a tcl script for this (shown below):
>>>>
>>>> set frames [molinfo top get numframes]
>>>> set fp [open "LIG.txt" w]
>>>> set protein "resid 1 to 442"
>>>> for {set i 0} {$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.Vasista
>>> M.Tech,Department Of Chemical Engineering,
>>> IIT Guwahati.
>
>
> --
> A.Vasista
> M.Tech,Department Of Chemical Engineering,
> IIT Guwahati.