Hi Emmett,
Thank you for the informative reply. I found a thread saying the NetCDF plugin is not developed yet for Mac Catalina, which is my OS.
But your second method served my purpose for now.
——
Jatin Kashyap
> On Sep 11, 2020, at 1:29 AM, Emmett Leddin <drtigger13.gmail.com> wrote:
>
>
> Hello Jatin,
>
> This part of the tutorial refers to visualizing the structures using a different program. Most people accomplish that by using VMD (https://www.ks.uiuc.edu/Research/vmd/).
>
> The nc extension is used for the NetCDF file format. VMD has a NetCDF plugin, and if that has been installed you can do “vmd -parm7 file.prmtop -netcdf file.nc” to open it (or specify it using the File Load GUI). If I remember correctly, the NetCDF plugin isn’t supported on Windows machines.
>
> The final frame (so what should be at 300 K) is saved in the .rst file. You can also load just that file using “vmd -parm7 file.prmtop -rst7 file.rst”. Hope that helps!
>
> Sincerely,
>
> Emmett Leddin
>
> Pronouns: he/him
> Chemistry PhD Candidate
>
>
>>> On Sep 10, 2020, at 23:36, Jatin Kashyap <jk435.njit.edu> wrote:
>> Dear AMBER Community,
>>
>> I am following the protein-ligand tutorial.[1] I was able to reproduce it until the last step. But I am not able to visualize the binary trajectory file generated in the very last step (.nc).
>> As this is the first time I came across this file format. Can anybody please guide how to follow the last part of the instructions.[2]
>>
>> Thank you very much.
>>
>>
>> [1]
>> https://ambermd.org/tutorials/basic/tutorial4b/index.html
>>
>> [2]
>> “you can take a look at the snapshot at 300K"
>>
>> ——
>> 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 Mon Sep 14 2020 - 14:30:02 PDT
