Good morning,
my name is Sebastian Franco-Ulloa, and I was wondering if you could help me with an error I am getting while trying to run a MMPBSA calculation. I extracted a frame (in pdb format) from an MD simulation of a protein-DNA-ligand-solvent system. From that frame I generated 4 structures: the complete solvated system, the system without ions and water, the receptor (protein and DNA), and the ligand. Then I used tleap to create prmtop files for these four structures, and it worked fine. The problem arises when executing the MMPBSA.py script. Apparently, it properly reads the topology and structure files, but when it starts the GB calculation it exits with the following error:
CalcError: /PATH/sander failed with prmtop com.prmtop!
com.prmtop is the topology file of the system without water and ions.
I appreciate very much all the help you could provide me with.
Best,
Sebastian Franco Ulloa
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Received on Mon Sep 11 2017 - 02:00:03 PDT
