[gmx-users] Re: Ligand_charges

[pkmukher]

Dr Spoel,

  Thanks for your suggestions. Actually i would be using the
GROMOS96 force field(option 0 in pdb2gmx GROMOS96 43a1).I am
new to the GROMACS package.I wish to simulate a
ligand-protein system and had been using the drug-enzyme
tutorial available for this purpose. In the tutorial they
use the PRODRG2 server to generate the ligand structure
files. I find that the charges were calculated for a
structure with only polar hydrogens present. This is then
used to form the ligand-protein complex and solvation,
neutralization etc.I was wondering

1) which ligand file should i use to generate my gaussian
inputs. one with all the hydrogens or one with just the
polar hydrogens.

2) I presume that for the gaussian calculation I have to
submit an all hydrogen structure. In that case how do I
refit the charges onto the polar hydrogen only structure
which i will use for the generataion of the ligand-protein
complex(as per the tutorial)

3) Do you think that the current forcefield is good for
simulation of ligand-protein complexes.

Kindly help me with your suggestions.Thanks so much  

Prasenjit Kumar Mukherjee
Graduate Student
Department of Medicinal Chemistry
School of Pharmacy
University of Mississippi
USA

Cell   - 662 380 0146
Office - 662 915 1286