Hi Duan,
it looks like sander.APBS is getting wrong dimensions of the molecule,
somehow. Can you send me the input files (off the list) so I can try to
reproduce it and see what's going on?
Thanks,
Robert
On Fri, Nov 16, 2012 at 09:31:18AM +0800, baogen duan wrote:
> 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 - 21:30:02 PST
