[AMBER] MMPBSA calculation in complex with Membrane

From: 徐见容 <gjtigergj.163.com>
Date: Mon, 18 Jul 2011 00:43:29 +0800

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 MMPBSA.py 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 ante-MMPBSA.py, 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.



Jian-Rong Xu (徐见容), 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: janker.xu.gmail.com
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Received on Sun Jul 17 2011 - 10:00:02 PDT
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