Hi all,
I am trying to estimate the binding free energy of a ligand (steroid) to
a protein using MMPB/SA & MMGB/SA approaches. I am using MMPBSA.py
available in amber 11. I followed the amber tutorials. My GB calculation was
successful but the PB calculation failed. The ourput of the
_MMPBSA_complex_pb.mdout & _MMPBSA_receptor_pb.mdout shows the following
error message:
4. RESULTS
--------------------------------------------------------------------------------
POST-PROCESSING OF TRAJECTORY ENERGIES
trajectory generated by
ptraj
minimizing coord set # 1
PB bomb in pb_reslist(): maxnbr too small
Please let me know how can I fix this error.
2. I have another naive question. I got binding free energy (delta G) from
MMGB/SA calculation. Now I want to estimate the binding affinity in nM unit.
How can I do it?
Thanks
Chanchal
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Received on Tue May 25 2010 - 07:00:06 PDT
