[Chimera-users] Setting a pathway/trajectory for a molecule

[Rani Wiswedel]

Hi Elaine

Thank you very much for your quick reply. I don't think I will be running the actual simulations on Chimera, I was just told to set up the pathway of the substrate through the pore; specify points that would create a pathway for the substrate to travel through the pore structure. Would this be possible?

I also looked at the Volume Path Tracer, but this doesn't seem to be appropriate either?

Thank you again

Regards,
Rani


On Fri, 18 Sep 2020, 22:26 Elaine Meng, <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>> wrote:
Hi Rani,
Chimera is not the right program to do something like this.  Please see the discussion from earlier today, shown in these links:

<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-September/017228.html>
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-September/017234.html>

As mentioned in those posts, it is not appropriate for larger systems or when long simulations are needed.  Also it does not have any options for guiding sampling along a path or for calculating free energies.  Some other programs you might consider for running molecular dynamics calculations are given in those posts.

That tutorial you mention is not about running any molecular dynamics simulation.  It only gives an example of looking at molecular dynamics results that were saved from another program (AMBER) that actually did the calculations.

Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 18, 2020, at 12:56 PM, Rani Wiswedel <wswran001 at myuct.ac.za<mailto:wswran001 at myuct.ac.za>> wrote:
>
> Good day,
> I am an honours student attempting to set up my first molecular dynamics simulation, and am having some trouble trying to understand how to set a pathway for a substrate through a pore in Chimera. I am very unsure of how to do this, and was wondering if you could provide some help. I tried following the Trajectory and Ensemble Analysis tutorial, but essentially cannot get past the first step of downloading leap.top etc. I am also not sure if this is the correct tutorial to follow for what I am looking to do?
> Any advice would be greatly appreciated, I am in way over my depth.
> Thank you
> Kind regards,
> Rani
>

Disclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at http://www.uct.ac.za/main/email-disclaimer or obtainable from +27 21 650 9111. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via https://csirt.uct.ac.za/page/report-an-incident.php.

Disclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at http://www.uct.ac.za/main/email-disclaimer or obtainable from +27 21 650 9111. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via https://csirt.uct.ac.za/page/report-an-incident.php.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20200918/8e1c723b/attachment-0001.html>