Hello All,
I need a help regarding parametrization of ligand (small molecule) using
AMOEBA potential. I am following the article " Calculation of protein–ligand
binding free energy by using a polarizable potential" 2007.
I am able to parameterize the protein part using "leapamoeba" for ligand I
am facing problem.
Till date, I used Gaussian 03 for geometry optimization (HF/6-31G*) and
single point energy calculation using MP2/6-311++G(2d,2p) level. The
electrostatic parameters, including monopole, dipole and quadrupole moments,
were derived from the density matrix using GDMA v2.2. I am stuck after this
step...as I dont know how to get van der Walls, bond, angle, and atomic
polarizability parameters of the ligands using AMOEBA potential
(amoebapro.prm) available in TINKER.
Now should take the .xyz file (output obtained using poledit of Tinker) and
convert it to .pdb and take it to AMBER...for parameterization?..as, analyze
(Tinker) is not running, leading to error " MECHANIC -- Some Required
Potential Energy Parameters are Undefined TINKER is Unable to Continue;
Terminating the Current Calculation".
Kindly guide me
Thanks in Advance
--
--
SUNITA GUPTA
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Received on Tue Aug 03 2010 - 05:00:06 PDT
