[Dock-fans] Combining DOCK with AMBER

[Francesco Pietra]

I posted previously that, with DOCK6.1, dock-prep for my protein, after
repeated fixing, arrived at fractional charges for the residues. Either some
were still misnamed, or some were lacking. This was the best I could do.

Accepting the suggestion to go to Amber (someone was even skeptical that the
fractional charges for this large receptor could be assigned by Antechamber), I
have now loaded the pdb to leap (Amber9), whereby heavy atoms were added (where
I had set TER records) and H/lone pairs also added. Both prmtop and inpcrd
could be saved (and opened correctly with VMD). Of perhaps major concern
(leap.log attached):

(Residues lacking connect 0/ connect 1 -
These don't have chain types marked:
res  total affected
CTHR 4
NSER 4

Should all that be OK, how to go to DOCK now? I have prmtop and inpcrd files
also for the ligand, obtained from prepare_amber.pl, though, obviously, no such
files for the complex receptor-ligand.

Also, the receptor has 24.000000 charge: should docking be carried out with
this charged receptor or should it be first neutralized (in leap?).

I realize that this a combination of tricky problems and my limited experience.
Thanks for your understanding.

francesco pietra

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