Dear all,
I used MMPBSA.py in AmberTools 1.5 combined with Amber 11 to calculate binding free energy, In the course of PB calculation, sander.APBS program was used.
Due to large value of "fglen" and "cglen" initiation in the PB calculation, it resulted in large grid points which exceeds the maximum. The initiation parameter of PB in _MMPBSA_complex_pb.mdout file is as following:
iAPBS: Using charge/radii definition from prmtop file
iAPBS: Grid dime not specified, calculating ...
iAPBS: Requesting dime re-calculation on the fly
iAPBS: Grid values:
iAPBS: fglen: 616.300 616.300 616.300
iAPBS: cglen: 1013.7101013.7101013.710
iAPBS: dime: 124912491249
iAPBS: grid: 0.500 0.500 0.500
iAPBS: Required memory (in MB): 371635.656
But for the our studied system, the largest distance of two atoms is about 10 nm. The initiated parameter of PB should be less than the present value. Could anyone give me some help about this problem? Thank you for your great help!
Best wishes,
Yours Sincerely,
Duan Baogen
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Received on Thu Nov 15 2012 - 05:30:04 PST
