Hi Jason,
Thank you for your help. I indeed did it in a wrong way.
I still have some problems and maybe because I use 'chamber' in a wrong way. I convert the pdb and psf files to prmtop in the following way.
I know when calculating the MMPBSA I must have four prmtop files, for the solvated system, the complex, the receptor and the ligand. I had the pdb and psf files for the solvated system. And I saved the pdb and psf files for the complex, receptor and ligand from the solvated system in VMD. Then I converted the files to prmtop files using chamber. But when run the MMPBSA.py, it seemed that the prmtop files of the solvated system, the complex, the receptor and the ligand were not compatible.
What is the right way to do that? Please help me.
Thank you very much.
Ying
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Received on Tue Jan 21 2014 - 19:00:03 PST
