Depends on what you mean by docking. Performing an actual docking simulation? Not as far as I am aware, no
You can couple VMD with NAMD and perform “interactive MD” simulations. I assume this could be used to do some regular/steered MD and minimisation to fit something into a binding pocket.
Otherwise, dock6/autodock/vina are alternative solutions.
Best regards
// Gustaf
> On 16 Mar 2021, at 10:39, ışılay öztürk <isilayozturk.gmail.com> wrote:
>
> Actually, I have a question also about VMD.
> Is it possible to docking the drug into the DNA interface with VMD? or how?
> My aim to use (and prepare) it for QM/MM.
>
> If someone give me some advice, I will be grateful
>
> Thank u in advance
>
> Işılay Öztürk
>
> isilayozturk.gmail.com
>
> Jatin Kashyap <jk435.njit.edu>, 16 Mar 2021 Sal, 06:23 tarihinde şunu yazdı:
>
>> 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
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> --
> *_______________________*
>
> *PhD. Student Işılay Öztürk*
>
> *EGE UNIVERSITY Graduate School of Natural and Applied ScienceDepartmant of
> Chemistry / Physical Chemistry35100 Bornova / IZMIR / TURKEY*
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Received on Tue Mar 16 2021 - 03:00:02 PDT
