Re: [PyMOL] Amber .nc

[Stejskal, L. <len...@uc...>]

I had to change the trajectory into .mdcrd and took the take care of the box I believe. I am not sure you can keep .nc format without the truncated octahedron tbf.


Thank you!


Lenka

________________________________
From: Mateusz Bieniek <bie...@gm...>
Sent: 23 July 2018 14:28:12
To: Stejskal, Lenka
Cc: pym...@li...
Subject: Re: [PyMOL] Amber .nc

Can you share what error/message you get when you try to load the trajectory with the command?

The snippet of code I shared works for me. According to this page it should just work: https://pymolwiki.org/index.php/Load_Traj
Load Traj - PyMOLWiki<https://pymolwiki.org/index.php/Load_Traj>
pymolwiki.org
load_traj loads a trajectory as "states" into an already loaded molecular object.. Since version 1.0, PyMOL uses the Molfile Plugin backend, which supports a variety of trajectory file formats.



Do you happen to use a truncated octahedron?

Best, Mat

On Mon, Jul 23, 2018 at 2:27 PM Stejskal, Lenka <len...@uc...<mailto:len...@uc...>> wrote:

Hi Mat,


I have of course read that but I am still unable to load the trajectory. I was looking for an actual successful example not just a guide.


Thanks


Lenka

________________________________
From: Mateusz Bieniek <bie...@gm...<mailto:bie...@gm...>>
Sent: 23 July 2018 14:04:22
To: Stejskal, Lenka
Cc: pym...@li...<mailto:pym...@li...>
Subject: Re: [PyMOL] Amber .nc

Hi Lenka,

Let me first state that the command "help load_traj" points to the webpage which in turns says that the .nc format is supported by pymol.

I come from the gromacs background. Once you load the topology/state of your system (in my case .gro or .pdb), then use "load_traj", ie
load_traj trajectory.nc<http://trajectory.nc>

There are other options for this command (start, end, shift, etc).

Hope this helps, Mat

On Mon, Jul 23, 2018 at 11:42 AM Stejskal, Lenka <len...@uc...<mailto:len...@uc...>> wrote:

Dear Pymol users,


Can somebody advise how I can open amber trajectory file in .nc format?


Thank you


Lenka

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