Hi all:
I make some molecules dock to protein, the result is
grid score:
vdw:
es:
but sometime, the es=0.0000 vdw = grid score
Grid Score: -59.719940
vdw: -59.719940
es: 0.000000
generally, the results of grid score/vdw/es are different each other.
Grid Score: -81.593117
vdw: -66.652908
es: -14.940211
I use the same dock.in file, but the result is different, why??
Thank for u help!!
GuanXin
2008.03.20
the following is my dock.in
ligand_atom_file a.mol2
limit_max_ligands no
skip_molecule no
read_mol_solvation no
calculate_rmsd yes
use_rmsd_reference_mol no
orient_ligand yes
automated_matching yes
receptor_site_file
selected_spheres.sph
max_orientations 500
critical_points no
chemical_matching no
use_ligand_spheres no
flexible_ligand yes
min_anchor_size 40
pruning_use_clustering yes
pruning_max_orients 100
pruning_clustering_cutoff 100
use_internal_energy yes
internal_energy_att_exp 6
internal_energy_rep_exp 12
internal_energy_dielectric 4.0
use_clash_overlap no
bump_filter no
score_molecules yes
contact_score_primary no
contact_score_secondary no
grid_score_primary yes
grid_score_secondary no
grid_score_rep_rad_scale 1
grid_score_vdw_scale 1
grid_score_es_scale 1
grid_score_grid_prefix grid-ch3
dock3.5_score_secondary no
continuous_score_secondary no
gbsa_zou_score_secondary no
gbsa_hawkins_score_secondary no
amber_score_secondary no
minimize_ligand yes
minimize_anchor yes
minimize_flexible_growth yes
use_advanced_simplex_parameters no
simplex_max_cycles 1
simplex_score_converge 0.1
simplex_cycle_converge 1.0
simplex_trans_step 1.0
simplex_rot_step 0.1
simplex_tors_step 10.0
simplex_anchor_max_iterations 500
simplex_grow_max_iterations 500
simplex_final_min no
simplex_random_seed 0
atom_model all
vdw_defn_file vdw.defn
flex_defn_file flex.defn
flex_drive_file flex_drive.tbl
ligand_outfile_prefix e1
write_orientations no
num_scored_conformers_written 1
rank_ligands no
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