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 - 08:00:05 PDT
