Re: [AMBER] MMPBSA calculation in complex with Membrane

From: Bill Miller III <>
Date: Sun, 17 Jul 2011 12:47:16 -0400

Does the calculation fail immediately, or does the GB calculation actually
progress before dying? You can check the _MMPBSA*mdout files to see if an
error is written to those files. Was there any error or warning messages
written to the screen when you were running the calculation? You almost
might want to look though the _MMPBSA*ptraj*out files to see if ptraj was
able to correctly read in your trajectory using the provided topology files.


2011/7/17 <>

> Dear all,
> I built a complex of GPCR and a small molecule ligand (X), then inserted
> them into a POPC membrane. After 20ns' MD, I tried to use to
> calculate the delta binding energy. Topology files are
> complex+Membrane+solvated, complex, GPCR and ligand (X). The topology files
> are generated from complex+Membrane+solvated by, or by the
> pdb files before inserting complex into membrane.
> However, the calculation failed. The error occurs during GB calculations,
> for mmpbsa_py_energy or sander. There's no more debuging information even in
> the temporary files.
> So, is there someone who met this error before? Or, can someone provide a
> way to calculation binding energy in membrane system?
> Thanks a lot.
> Janker
> 2011-07-18
> Jian-Rong Xu (), PhD Student.
> Room 508, Building 3, Pharmacology Department
> Shanghai Jiao Tong University School of Medicine
> 280 South Chongqing Road
> Luwan District,Shanghai, P.R.China 200025
> Mobile: +86 186 2168 6069
> Email:
> _______________________________________________
> AMBER mailing list

Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Sun Jul 17 2011 - 10:00:03 PDT
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