ADL: High Torsional Free energy of ligand - please help

Guili Zhu liebely at
Tue Nov 13 10:11:20 PST 2007

Dear AutoDockers,

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 mailing list