Thank you Hai for sharing the link, nice presentation.
I don’t know why but the NetCDF issue in VMD and how to load files were raised raised in the amber, vmd and chimera lists yesterday and apparently the trajectory conversion suggestion was in a completely different forum, as well as the description regarding how to load files in chimera.
Best regards
// Gustaf
> On 17 Mar 2021, at 17:47, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
> 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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Received on Thu Mar 18 2021 - 02:30:03 PDT
