Thank you very much Gustaf for all your help. May you have a very good day.
Best,
Karla
On Wed, 23 May 2018, 00:49 Gustaf Olsson, <gustaf.olsson.lnu.se> wrote:
> Go to
>
> https://www-s.ks.uiuc.edu/Research/vmd/
>
> Download and install the correct version for your OS, simple as mounting
> the image and drag-n-drop, like any other software.
>
> If you want to launch VMD from the terminal, open up a new terminal window
> and do this:
>
> cd $HOME
> vi .profile
>
> push the “i” key on your keyboard and make sure that -- INSERT -- is
> displayed in the bottom left corner (or whatever you language settings
> might correspond to).
> Use your arrow keys to navigate to a new empty line at the end of this
> file (that might be empty BTW) and copy-paste the following lines or just
> the top one.
>
> alias vmd="/Applications/VMD\
> 1.9.3.app/Contents/Resources/VMD.app/Contents/MacOS/VMD"
> alias vmdtxt="/Applications/VMD\ 1.9.3.app/Contents/vmd/vmd_MACOSXX86"
>
> This is if you install the 1.9.3 version, otherwise change to 1.9.2 before
> pasting and saving. The first line will allow you to launch the VMD GUI
> window just as if opening it from you applications folder or launchpad. The
> second line launches a command line interface without GUI or graphical
> representation (sometimes useful for analysis).
>
> After pasting the first or both of these lines, hit the ESC key and note
> that the -- INSERT -- indicator disappears. Then hold down shift and press
> the “z” key on your keyboard twice (shift+z+z), this will save and exit.
> Don’t forget to either source your profile (source .profile) or quit the
> terminal and relaunching it for these changes to take effect.
>
> // Gustaf
>
> > On 23 May 2018, at 08:53, Karla Galdamez <kmgaldam.ucsc.edu> wrote:
> >
> > Dear Gustaf,
> >
> > I am running MacOs 19.12.2 Sierra. I have not individually installed VMD
> > only Amber Tools and 16. I thought VMD was included. If not, where is
> the
> > best place to download VMD?
> >
> > Thank You!
> > Karla
> >
> > On Tue, 22 May 2018, 23:05 Gustaf Olsson, <gustaf.olsson.lnu.se> wrote:
> >
> >> What OS are you using and how was VMD installed?
> >>
> >> // Gustaf
> >>
> >>> On 23 May 2018, at 05:43, Karla Galdamez <kmgaldam.ucsc.edu> wrote:
> >>>
> >>> Hello,
> >>>
> >>> I hope you are well! I am trying to activate a VMD window to reformat
> a
> >>> restart.rst file, would anyone share how to bring forth the VMD window
> >> from
> >>> the command line?
> >>>
> >>> Thank you!
> >>> Karla
> >>>
> >>> On Tue, May 22, 2018 at 5:32 PM, David A Case <david.case.rutgers.edu>
> >>> wrote:
> >>>
> >>>> On Tue, May 22, 2018, Sadegh Faramarzi Ganjabad wrote:
> >>>>>
> >>>>> Thanks for replying. Those atoms are actually parts of a water
> >> molecule.
> >>>>> That's why I'm surprised, if AMBER allows an H-H bond why it gives
> that
> >>>>> error? Can't it be because in the original psf file those extra bonds
> >>>>> already exist?
> >>>>
> >>>> We need more information, as I mentioned earlier: how exactly did you
> >>>> convert CHARMM to Amber format, and what version of AmberTools are you
> >>>> using? (Problems with waters in earlier versions have been fixed.)
> >>>>
> >>>> ....dac
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>>
> >>>
> >>>
> >>> --
> >>> Karla M. Galdamez, Ph.D
> >>> Research Fellow
> >>> Chemistry and Biochemistry Department
> >>> kmgaldam.ucsc.edu
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >> _______________________________________________
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> >>
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>
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Received on Wed May 23 2018 - 07:30:02 PDT
