Dear James,
I will try to get it done during the weekend - I'll get back to you once
it's ready.
Best,
Paolo
On 11/26/2013 05:51 PM, James Davidson wrote:
Dear All,
I think this is probably one for Paolo -- I was looking at fixing
certain atoms during MMFF minimisation, but couldn't find the
option... Then I re-read the UGM slides, and found the one titled
"Force-field wish list", and "fixed atoms" were one of the listed items!
My intended use-case is the following:
1.Load protein-ligand complex into PyMOL
2.Make some changes to the bound ligand (using the Builder functionality)
3.Select atoms that are allowed to move (manual selection, then use of
PyMOL's 'flag' command)
4.Pass the molecule over to RDKit (already incorporated in a plugin we
use), to minimise and then pass back (either as a new object, or apply
the new coordinates to the existing object in situ)
Actually, this process is already well-used by some of our chemists
here -- as a way of doing some simple modelling / idea exploration --
but is currently using a much 'flakier' MMFF implementation. So I
would definitely like to move to RDKit for the minimisation -- any
idea when a 'fixed atoms' option is likely to be added?
Kind regards
James
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