Dear All,
I want to run mmpbsa calculations of a protein docked with a small organic ligand. I have parametrize the ligand as follow
1. Converted mol file (originally created in hyperchem) to gaussian input file
2. Obtained Gaussian output file after Gaussian calculations.
3. run the antechamber and obtained a mole2 file from Gaussian output .
4. run the parmchk and obtained the frcmod file
5. Finally I have created prmtop and inpcrd files for ligand
I can run simulation on ligand and on both protein alone. Now I wish to run simulations with the protein ligand complex. I tried docking ligand mole2 (file obtained with antechamber from Gaussian output) with protein using Gold but Gold do not recognise this mole2 file. I tried opening this mole2 in hyperchem and unable to open this file as it complain not in correct format.
However I am able to dock original mol file with protein. But I can load this mol file with frcmod file obtained with mole2 file.
Please suggest me at this stage how I can make a complex which can be used with amber for mmpbsa.
Regards
Imtiaz
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Received on Sun Feb 07 2010 - 16:30:02 PST
