There is though they “hid” this option by separating MD files from static molecular files:
Tools -> MD/Ensemble Analysis -> MD Movie
You’ll get a popup where you enter Prmtop and Trajectory files and load.
Water is hidden by default unless associated with any “non water” in the system.
Some “doc” info: https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html
and a tutorial: https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html
In the end I guess that you will be using Chimera for visualisation and figures rather then analysis, which is primarily done with cpptraj. This is the way I have been using chimera. In my personal opinion, chimera is able to produce more versatile and higher quality graphics then VMD, which I normally use for visual inspection and some analyses rather then generating graphics.
Best regards
// Gustaf
On 17 Mar 2021, at 02:20, Jatin Kashyap <jk435.njit.edu<mailto:jk435.njit.edu>> wrote:
Hi Gustaf,
You got it right! I am sorry for not providing additional information in the first place.
I am using macOS, and it is mentioned in the VMD’s docs that NetCDF functionality is not supported on macOS Catalina.
I am working through UCSF Chimera, but there is no Amber param file format available to load the file as I try to load the parameter file.
Is there any tutorial that I can follow for analyzing the Amber trajectory with UCSF Chimera?
Thank you.
——
Jatin Kashyap
Ph.D. Student
Dr. Dibakar Datta Group
Department of Mechanical and Industrial Engineering
New Jersey Institute of Technology (NJIT)
University Heights
Newark, NJ 07102-1982
Phone- (201)889-5783
Email- jk435.njit.edu<mailto:jk435.njit.edu>
On Mar 16, 2021, at 4:00 AM, Gustaf Olsson <gustaf.olsson.lnu.se<mailto:gustaf.olsson.lnu.se>> wrote:
Without additional information, helping identifying potential problems will be hard.
If you, like me, are using a mac, there is still no support for NetCDF format in VMD in version vmd 1.9.4a48-Catalina-Rev7. I do not know if this support has been dropped in windows/linux versions as well or if this only affects macOS. If this is the case then one recommendation would be to use some other software, like UCSF Chimera, which supports NetCDF on macOS.
If not, then check the content of the “out” file for errors. There are also likely some useful tools available to check the integrity of trajectory files as well, cpptraj may have some tools, parmed maybe.
Best regards
// Gustaf
On 16 Mar 2021, at 05:23, Jatin Kashyap <jk435.njit.edu<mailto:jk435.njit.edu>> wrote:
Dear AMBER Community,
I am trying to visualize a .nc file in VMD by following a tutorial[1]. The tutorial visualization works fine but when I try the same steps with my own files [2], it throws following error:
Problem reading CRD file
Info) Finished with coordinate file .../short_traj.nc
Can anybody please help to understand what is wrong with my approach.
Thank you.
[1]
https://ambermd.org/tutorials/basic/tutorial2/section6.htm <
https://ambermd.org/tutorials/basic/tutorial2/section6.htm>
——
Jatin Kashyap
Ph.D. Student
Dr. Dibakar Datta Group
Department of Mechanical and Industrial Engineering
New Jersey Institute of Technology (NJIT)
University Heights
Newark, NJ 07102-1982
Phone- (201)889-5783
Email- jk435.njit.edu<mailto:
jk435.njit.edu>
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Received on Wed Mar 17 2021 - 01:00:02 PDT
