I am extremely thankful to you Jodi for giving your precious time to my
problem. And I am extremely grateful for such a detail and extremely
helpful explanation of the method. This is all what I needed to know.
Thanks a lot.
Thanks a lot to Dr. Case as well.
Best Regards
Asma
On Thu, Jun 28, 2012 at 7:42 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Thu, Jun 28, 2012, Jodi Ann Hadden wrote:
> >
> > First I had to rebond all your atoms -- I did this by looking at your
> > structure in VMD to compare and drawing all the bonds between atoms back
> > in using xleap's "Draw" tool found in the Manipulation section along the
> > top of the window. There is maybe an easier way to do this step, but I
> > was used to "drawing" drug molecules almost entirely from scratch, so
> > this was just the approach I used.
>
> There is a "bondbydistance" command, which usually does a good job of
> connecting atoms (assuming a reasonable initial geometry). But this is
> just
> a potentially easier way: what Jodi describes is fine.
>
> [Thanks to Jodi for taking the time to write a detailed description: this
> summarizes things that experienced users know, but which can be
> non-obvious to
> newcomers.]
>
> ....dac
>
>
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Received on Thu Jun 28 2012 - 21:00:02 PDT
