On Fri, Sep 11, 2015 at 4:21 PM, Eric Berquist <erb74.pitt.edu> wrote:
> Hi all,
>
> I've got a small peptide, and I'd like to add individual water molecules
> one at a time to see their affect on the peptide dynamics. What's the
> optimal way to place the waters randomly without having them overlap? As I
> expected,
>
> solvated_peptide = combine {peptide TP3 TP3 TP3 TP3}
> places the 4 TIP3P waters right on top of each other.
>
> Ideally, I'd be able to do this entirely within leap; it's fine that the
> placement would be random.
>
tleap doesn't have any faculty for doing this easily that I'm aware of.
You can apply translations and set positions of units, I believe, but this
is probably something you will want to script (i.e., have a script generate
a leap script for you).
You should play around with some of the options in tleap -- particularly
"translate" -- to see if you can get it to behave the way you want.
T
hen you can scale up
with a Python script or something.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Sep 11 2015 - 16:00:03 PDT
