[Dock-fans] Fwd: Amberscore after MD

Francesco Pietra 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

limit_max_ligands                                            no
skip_molecule                                                no
read_mol_solvation                                           no
calculate_rmsd                                               no
orient_ligand                                                no
flexible_ligand                                              no
bump_filter                                                  no
score_molecules                                              yes
contact_score_primary                                        no
contact_score_secondary                                      no
grid_score_primary                                           no
grid_score_secondary                                         no
dock3.5_score_primary                                        no
dock3.5_score_secondary                                      no
continuous_score_primary                                     no
continuous_score_secondary                                   no
gbsa_zou_score_primary                                       no
gbsa_zou_score_secondary                                     no
gbsa_hawkins_score_primary                                   no
gbsa_hawkins_score_secondary                                 no
amber_score_primary                                          yes
amber_score_secondary                                        no
amber_score_receptor_file_prefix                        protein (with
all hydrogen atoms in place)
amber_score_movable_region                                everything
amber_score_before_md_minimization_cycles                    100
amber_score_md_steps                                         3000
amber_score_after_md_minimization_cycles                     100
amber_score_gb_model                                         5
amber_score_nonbonded_cutoff                                 18.0
amber_score_temperature                                      300.0
ligand_outfile_prefix                                        output
write_orientations                                           no
num_scored_conformers_written                                1
rank_ligands                                                 no

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?

francesco pietra

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