Dear all,
In the courese of MMPBSA calculation, I used sander.APBS
(AmberTools1.5 and Amber 11) to calculate solvation free energy. But it
failed. the error message is:
* VaccSurf_ctor: Error! The requested number of grid
points (11360060) exceeds the maximum (50000)!
VaccSurf_ctor: Please check the variable MAX_SPHERE_PTS
to reset.*
* *
* *Then I checked the _MMPBSA_complex_pb.mdout file, it is found
that the iAPBS initiated parameter gives a large value for "fglen" and
"cglen" term, the detailed information is:
* iAPBS: Initializing APBS interface*
*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: 1013.710 1013.710 1013.710*
*iAPBS: dime: 124912491249*
*iAPBS: grid: 0.500 0.500 0.500*
*iAPBS: Required memory (in MB): 371635.656*
**
and the input parameters for PB calculation shown in _MMPBSA_pb.mdin file
are:
* File generated by MMPBSA.py*
*&cntrl*
* nsnb=99999, ntb=0, cut=999.0, imin=5,*
* igb=6,*
*/*
*&apbs*
* srfm=1, grid=0.5,0.5,0.5,*
* ionc=0.1,0.1, pdie=1.0, ionq=1.0,-1.0,*
* bcfl=2, nion=2, calc_type=0,*
* sdie=80.0, gamma=0.02267728,*
* ionrr=2.0,2.0,*
*/*
But the large measured distance of two atoms is about 10 nm. what is the
problem with this? Would you like to give me some help? Thank you!
Best wishes,
Yours sincerely,
Duan Baogen
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Received on Thu Nov 15 2012 - 18:00:03 PST
