Re: [AMBER] amber trajectory visualization issue:

From: Dr. Anselm Horn via AMBER <>
Date: Fri, 3 Nov 2023 12:27:37 +0100


it is not clear (to me) what your intention is:

When you have simulated a protein-ligand complex, you can read in the
corresponding file pair of netcdf and parmtop into VMD to visualize the
trajectory (you can, of course, read in several netcdf files).

In VMD, you can then visualize the trajectry, i.e. "run the movie":
it is a list of coordinate sets of your simulation, thus each snapshot
represents a structure.

For a detailed analysis of the interactions between the protein and the
ligand, you may use methods from cpptraj or even VMD itself.
Different visualization types can be achieved within VMD; have a look
into its manual (selections, representations) - the same holds for the
analysis features of cpptraj and the Amber manual.

Maybe this helps.



Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)

Am 03.11.2023 um 09:39 schrieb Kankana Bhattacharjee via AMBER:
> Dear AMBER users,
> I want to visualize the amber trajectory to visulize the protein ligand
> interactions and also to identify the active site residues (without waters
> in the structure). For that, I have complex.prmtop file, file,
> how can I visualize the static structure. Because after superimposing these
> two structures, vmd movie is generated. How can I visualize the simulated
> structure from the MD trajectory ? Which files do I require to do this ?
> Your suggestions would be appreciated.
> Thanks & Regards
> Kankana Bhattacharjee
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Received on Fri Nov 03 2023 - 04:30:03 PDT
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