Hi,
Yes. The end restart is the confirmation that you are looking for.
Satyajit
________________________________
From: Kankana Bhattacharjee <kankana.bhattacharjee_phd21.ashoka.edu.in>
Sent: 06 September 2023 12:04
To: SATYAJIT KHATUA <satyajitkhatua09.gmail.com>
Cc: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Visualizing amber MD trajectory in vmd:
I have traj.rst file. Are you talking about .rst file ?
[Mailtrack] <
https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> Sender notified by
Mailtrack<
https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> 09/06/23, 12:04:18 PM
On Wed, Sep 6, 2023 at 12:01 PM Kankana Bhattacharjee <kankana.bhattacharjee_phd21.ashoka.edu.in<mailto:kankana.bhattacharjee_phd21.ashoka.edu.in>> wrote:
Thanks. Basically, I want to visualize that, what are the protein residues that is interacting with the ligand at the end point. I have the whole trajectory in .nc format, but I think the end point conformation is most important.
[Mailtrack] <
https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> Sender notified by
Mailtrack<
https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> 09/06/23, 11:58:47 AM
On Wed, Sep 6, 2023 at 11:49 AM SATYAJIT KHATUA <satyajitkhatua09.gmail.com<mailto:satyajitkhatua09.gmail.com>> wrote:
Hi,
You can load a trajectory by browsing and loading your prmtop first. On top of that load your .nc file.
If you want to see the confirmation at the end then simply load .ncrst file instead of .nc file.
Best,
Satyajit
________________________________
From: Kankana Bhattacharjee via AMBER <amber.ambermd.org<mailto:amber.ambermd.org>>
Sent: 06 September 2023 11:38
To: AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
Subject: [AMBER] Visualizing amber MD trajectory in vmd:
Dear AMBER users,
I have performed MD simulation of protein ligand complex. Now, I want to
visualize the complex at the end point of simulation (say at 100 ns). How
can I do that job using VMD ?
Your suggestions would be appreciated.
Thanks & Regards
Kankana Bhattacharjee
_______________________________________________
AMBER mailing list
AMBER.ambermd.org<mailto:
AMBER.ambermd.org>
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 06 2023 - 00:00:02 PDT
