[Dock-fans] Fwd: Amberscore after MD
chiendarret at gmail.com
Sat Aug 16 00:16:38 PDT 2008
I forgot to ask about the number of steps for amberscore that may
hopefully lead to meaningful outputs. After flex docking, I used in
amber_score_receptor_file_prefix protein (with
all hydrogen atoms in place)
In order to re-run amberscore after MD in the membrane, how many
(minimum) steps may be suggested?
Thanks also for the answer to "How to read score outputs". I knew not
to be asking anything new, howver it is useful to have a comprehensive
illustration with an example.
---------- Forwarded message ----------
From: Francesco Pietra <chiendarret at gmail.com>
Date: Fri, Aug 15, 2008 at 9:47 PM
Subject: Amberscore after MD
To: dock-fans <dock-fans at docking.org>
For a protein and a ligand I carried out rigid docking, flex docking
and amberscore wirh DOCK6. Then, the complex protein-ligand was
embedded in a lipidic membrane for MD simulation with AMBER 10.
At this point, I would like to carry out amberscore again. Is it wise
to do that for the lowest_energy_structure captured from MD
trajectories with ptraj? If so, working out manually the pdb file,
extracting the parts related to the protein and the ligand for
"Prepare" with Chimera.
The alternative (which I tend to disfavor) is the averaged structure
from the MD simulation.
Or is anything better?
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