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
> >>
> >>
> >> _______________________________________________
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> >>
> >
> >
> >
> > --
> > 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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Received on Wed May 23 2018 - 00:00:02 PDT
