Thank u so much for your advices
Best regards
Işılay
Gustaf Olsson <gustaf.olsson.lnu.se>, 16 Mar 2021 Sal, 13:59 tarihinde şunu
yazdı:
> “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*
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >> _______________________________________________
> >> 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
> 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
Received on Tue Mar 16 2021 - 06:00:03 PDT
