[Dock-fans] amber_score

[Francesco Pietra]

I open a new thread (amber_score) because previous thread (Combining Dock with
Amber) was becoming too complex, in the hope to get some general guidelines.

To summarize

(1) With a pore protein model and a flexible 150-atoms ligand (working with
Dock6.1 and Chimera 17 Oct build) I could carry out both rigid_docking and
flex_docking along the default lines of the tutorials. The ligand is seen
inside the pore, roughly the same view in both cases.

(2) As prepared with Chimera, the protein did not allow to get (via dock-prep)
the prmtop and inpcrd files needed for amber_score. Therefore, I prepared the
protein with Leap in Amber9, getting prmtop and inpcrd, which allowed a correct
graphical representation in both Chimera and VMD.

(3) The pdb file for the protein created in Amber9 from prmtop and inpcrd with
ambpdb proved unsuitable for Chimera dock-prep (standard amino acids were
mis-viewed as non-standard residues and assigned to Antechamber, which wrongly
calculated fractional charge for the residues). I changed strategy, loading the
protein to Chimera from the Leap-created prmtop and inpcrd files. That also
failed (dock-prep), but for a different reason, Value Error: underlying C++
Molecule object is missing (I have documented that with an error.log on
previous thread), which I do not understand.

Now the files from Leap (2 above) allowed amber_scoring. I carried out both a
rapid (few minutes) "ligand" option and a longer (4 hours) "everything" option.
In both cases, from the complex "final_pose.amber.pdb", the ligand is immersed
into the protein, though not along the pore walls, unlike with the rigid and
flex docking mentioned in (1). The bad point is that the ligand was broken into
two major fragments, and minor CH2 fragments. At a rough inspection, the
protein does not appear to have suffered any major damage, in both options. I
must add that breakage of the ligand is surprising because it is a thermally
very stable molecule.

I am much confused about the line to follow for amber_score. As carried out
above, the receptor has no spheres, while the ligand mol2 file was taken from
the tutorial-like procedures. Does the receptor pass through the stages of
spheres/grid also for amber_score?

Hope to have made clear the general terms.

Thanks

francesco pietra



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