Re: [AMBER] Visualizing NetCDF in VMD - ERROR

From: <>
Date: Tue, 16 Mar 2021 09:49:59 +0100

For ubuntu (20.10/21/04) softwares with netcdf are very difficult to
build because apparently the package is no more in repos. I use chimerax
(ucsf chimera new version but not in place of) and pymol a bit easier to
use that VMD but less adapted than VMD (in fact I don't know well VMD
but it seems very powerfull and complecated when it's only for
visualizing a pdb like I often do ?)

Le 16/03/2021 à 09:00, Gustaf Olsson a écrit :
> 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 <> 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 .../
>> Can anybody please help to understand what is wrong with my approach.
>> Thank you.
>> [1]
>> <>
>> ——
>> 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-
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>> AMBER mailing list
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Received on Tue Mar 16 2021 - 02:00:01 PDT
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