[Dock-fans] Amber score

Rima Chaudhuri rima.chaudhuri at gmail.com
Fri Jul 6 15:03:44 PDT 2007


I am running  2 different sets of ligand conformations ( but of the same 30
molecules) for rescoring with amber_score.

A. Using the normal grid score to rank some 30 compound and then use these
conformations for rescoring with amberscore.I used the movable region as
'ligand' in case1 and 'distance' in case2. Case 1 runs fine. Case 2 however,
stalls at the following point

Molecule Library Output Parameters
ligand_outfile_prefix                                        out_dist
write_orientations                                           no
num_scored_conformers_written                        1
rank_ligands                                                    yes
max_ranked_ligands                                         30

these are the last few lines of the dock.out file, it is still running and
has been for the past 2.5 hrs w/o writing anything else. I want to know if
this is normal? I used the pre-md min steps as 100, md-steps of 5000 and
post md steps of 100. The movable cutoff was specified as 8.0 angstroms,
temperature 300K...any suggestions?

B. Using the same ligand set as in 1, I first ran them in GOLD and used
these conformations to re-score in dock_amber_score. Almost all the amber
scores are positive, whereas in the case of using grid score and then amber
re-scoring the amber scores were all negative values and suggested good
binding as expected. I understand that using the gold conformations and then
dock might cause this problem due to differences in energy terms and
parameters between Gold and dock_amber_score, but to keep things consistent,
is there a workaround this issue? meaning , if I wanted to make correlation
plots between the amberscore and experimental data, right now it is quite

If I stick to the conformations from grid_score ranking, the do not look so
good and the experimental correlation is only 18%. I would rather want to
have the gold conformations as the starting geometry! any suggestions that
can help me get non-positive binding energy using amber_score?


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