Dear Bill,
Thank you for your reply. But I still have some puzzle about
this. If I upgrade to AmberTools 12, whether should I correspondingly
upgrade Amber 11 to Amber 12?
I also have try some tests using sander program in Amber 11 to
carry out minimization or MD simulation, and the input prmtop and
inpcrd are generated by Chamber program. For the small ligand molecules,
minimization and MD is Ok. But for receptor and complex, the output file of
minimizaiton and MD shows the same error as MMPBSA calculation. the error
is also:
rdparm: a parameter array overflowed
(e.g. the table of dihedral params)
NUMBND = 133 max is 5000
NUMANG = 297 max is 900
NPTRA = 612 max is 1200
NATYP = 72 max is 100
NPHB = 0 max is 200
NTTYP = 2628 max is 1830
This is to show that minimizaion and MD simulation can not work. what is
the problem with this ? Thank you!
Best wishes,
Yours Sincerely,
Duan Baogen
2012/11/7 Bill Miller III <brmilleriii.gmail.com>
> I believe this has been fixed if you upgrade to AmberTools 12.
>
> -Bill
>
> On Tue, Nov 6, 2012 at 9:25 PM, baogen duan <dbaogen.gmail.com> wrote:
>
> > Dear all,
> >
> > I want to use CHARMM force field to carry out binding free energy
> > calculation through MMPBSA python script in AmberTools1.5. Using the
> > Chamber program, the corresponding " prmtop " files are generated. And
> then
> > use the following input file to calculate binding free energy:
> >
> > *&general*
> > * startframe=1, endframe=1, interval=1,*
> > * keep_files=1,strip_mdcrd=0,verbose=1,*
> > * use_sander=1*
> > */*
> > *&pb*
> > * istrng=0.1*
> > */*
> >
> > But calculation is interrupted due to sander error during PB
> calculations.
> > the error message in the _MMPBSA_complex_pb.mdout file is:
> >
> > rdparm: a parameter array overflowed
> > (e.g. the table of dihedral params)
> > NUMBND = 133 max is 5000
> > NUMANG = 297 max is 900
> > NPTRA = 612 max is 1200
> > NATYP = 72 max is 100
> > NPHB = 0 max is 200
> > *NTTYP = 2628 max is 1830*
> > **
> > Amber 11 and AmberTools 1.5 are used in the calculation.
> >
> > Would you like to help me with this problem? Thanks in advance!
> >
> >
> > Best wishes,
> > Yours Sincerely,
> >
> > Duan Baogen
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-846-1633
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Nov 07 2012 - 01:30:03 PST
