VMD-L Mailing List
From: Bassam Haddad (bhaddad_at_pdx.edu)
Date: Tue Jun 02 2020 - 12:33:03 CDT
- Next message: David Alejandro Rincón Daza: "PSFGEN"
- Previous message: Axel Kohlmeyer: "Re: Fw: Hbond extension"
- Maybe in reply to: Bassam Haddad: "Re: analyzing amino acids forming pore constrictions in a channel protein"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
Hi Yogesh,
You are welcome to any of the scripts you find from my lab's Github
<https://github.com/reichow-lab/Tcl-Scripts> page, and feel free to contact
me personally if you have questions regarding them. These two scripts aught
to help you:
HOLE-APBS_gen.tcl will create inputs for you for HOLE and APBS (you can
comment these out) from every frame that you have loaded into memory. Then
you can use serial_hole.sh to run Hole on all of your frames. From here
you'll just have to parse the data – there is an `awk` line in the script
that you can modify to retrieve whatever information you want.
Best,
Bassam
On Tue, Jun 2, 2020 at 10:08 AM Yogesh Sharma <yogesh.rma13_at_gmail.com>
wrote:
> Thank you sir,
> Sounds reasonable but I am new to md simulation s. I have used hole
> program for average pore diameter analysis over the trajectory. But I m
> not skilled enough to dig deep into codes. Do you have some script that you
> might have used earlier?
>
> On Tuesday, June 2, 2020, Bassam Haddad <bhaddad_at_pdx.edu> wrote:
>
>> Hi Yogesh,
>>
>> You can use Hole <http://www.holeprogram.org/> to calculate the minimum
>> pore radii at each z-height, this will tell you where the constriction is,
>> and which amino acid is contributing to the minimum radii. You'll just have
>> to parse the hole outputs.
>>
>> Best of luck,
>> Bassam
>>
>> On Tue, Jun 2, 2020 at 4:41 AM Yogesh Sharma <yogesh.rma13_at_gmail.com>
>> wrote:
>>
>>> greetings everyone,
>>> hope you guys are doing good.
>>> I am interested in finding amino acids that are forming constrictions in
>>> protein pore throughout trajectory. I can do it manually for asingle frame
>>> but i am more interested in variations throughout trajectory in that
>>> region. can someone suggest the way ?
>>>
>>> *with regards*
>>> *Yogesh Sharma*
>>>
>>>
>
> --
> * with regards*
> *Yogesh Sharma*
>
>
>
- application/octet-stream attachment: HOLE-APBS_gen.tcl
- text/x-sh attachment: serial_hole.sh
- Next message: David Alejandro Rincón Daza: "PSFGEN"
- Previous message: Axel Kohlmeyer: "Re: Fw: Hbond extension"
- Maybe in reply to: Bassam Haddad: "Re: analyzing amino acids forming pore constrictions in a channel protein"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]