“visual docking”
I would think this is possible with vmd though I have not tried it myself. Lining up structures isn’t always trivial though moving them around can be done in chimera or avogadro, likely numerous other software.
// Gustaf
> On 16 Mar 2021, at 11:00, ışılay öztürk <isilayozturk.gmail.com> wrote:
>
> I won't be used for calculation. Just I want to fix to drug into interface.
> Is there a program I can use for this purpose? I'm also open to other
> alternatives besides the VMD.
>
> Thank you for this advice "Otherwise, dock6/autodock/vina are alternative
> solutions."
>
> Best regards
>
> Işılay
>
> Gustaf Olsson <gustaf.olsson.lnu.se>, 16 Mar 2021 Sal, 11:50 tarihinde şunu
> yazdı:
>
>> 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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>>
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>
>
> --
> *_______________________*
>
> *PhD. Student Işılay Öztürk*
>
> *EGE UNIVERSITY Graduate School of Natural and Applied ScienceDepartmant of
> Chemistry / Physical Chemistry35100 Bornova / IZMIR / TURKEY*
> _______________________________________________
> AMBER mailing list
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Received on Tue Mar 16 2021 - 05:00:02 PDT
