On Tue, Mar 16, 2021 at 9:21 PM Jatin Kashyap <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?
>
>
If you are familiar with jupyter notebook and don't mind learning new
software, you can give nglview a try. (
https://github.com/nglviewer/nglview/blob/master/README.md)
nglview is not as powerful as VMD or Chimera but it's quite convenient for
visualization.
PS: See Lily's talk mentioning about the usage of nglview:
https://youtu.be/X5umNQDqfqQ?t=616
Cheers
Hai
> 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
>
> > On Mar 16, 2021, at 4:00 AM, Gustaf Olsson <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> 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
> >>
> >> _______________________________________________
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> >
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Received on Wed Mar 17 2021 - 10:00:02 PDT
