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*
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
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>
--
*_______________________*
*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 - 03:30:02 PDT
