ADL: High Torsional Free energy of ligand - please help
liebely at gmail.com
Tue Nov 13 10:11:20 PST 2007
May I have your attention for a problem that occurred during my dock,
When analyzing my *.dlg file, i realized that all the bound conformations
had high positive binding energy. It seems to be due to the initial high
torsional free energy of the unbound ligand:
Calculating normalized torsion vectors.
Number of atoms in ligand: 131
Number of vibrational degrees of freedom of ligand: 387
Number of torsional degrees of freedom = 90
Estimated loss of torsional free energy upon binding = +24.6960 kcal/mol
As a result of this, the docked energy of all conformations are like this:
DOCKED: MODEL 47
DOCKED: USER Run = 47
DOCKED: USER DPF = 26m1LA_hbb50.dpf
DOCKED: USER Estimated Free Energy of Binding = +20.19 kcal/mol
DOCKED: USER (1) Final Intermolecular Energy = -6.74 kcal/mol
DOCKED: USER vdW + Hbond + desolv Energy = -6.85 kcal/mol
DOCKED: USER Electrostatic Energy = +0.11 kcal/mol
DOCKED: USER (2) Final Total Internal Energy = -6.33 kcal/mol
DOCKED: USER (3) Torsional Free Energy = +24.70 kcal/mol
DOCKED: USER (4) Unbound System's Energy = -8.56 kcal/mol
Could you specialists let me know how to solve this? Should I do energy
minimization of the ligand?
If so, what energy minimization program is compatible with structures
containing rotatable bonds in .pdbqt format?
If not, what else can I do??
Looking forward to your reply! Many thanks!
p.s.: My ligand is a amphiphilic molecule containg two connected sugar rings
with phosphate groups attached to each, and with multiple acyl chains
attached to each ring (thus extremely flexible).
More information about the autodock