On Fri, Mar 18, 2016 at 2:02 PM, Arnoult, Eric [JRDUS] <EArnoult.its.jnj.com
> wrote:
> Dear Amber users,
>
> Have your tried using leap to place a ligand at different distances from
> its target? How to do it?
> Let say ... the center of mass of the ligand placed at different
> coordinates provided by the user.
>
I've done something like that using the xleap graphical interface, but
that was for a short organic polymer threaded inside a macrocycle. Not
more than 100 atoms total for the whole system. It was clunky, but it got
the job done.
(It was also a *long* time ago
)
If you're talking about a ligand and its target receptor, that usually
means there are many hundreds or thousands of atoms involved. If that's
the case, tleap is the wrong tool to use. You'll need a docking program to
do that.
HTH,
Jason
--
Jason M. Swails
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Received on Tue Mar 22 2016 - 19:00:07 PDT
