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
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
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Received on Wed May 23 2018 - 01:00:02 PDT
