On Tue, Nov 27, 2012 at 4:16 AM, colvin <colvin4367.gmail.com> wrote:
> Dear all,
>
> I have amber 12 now, but the decomposition still cannot be executed,
> the output remained:
>
>
> rdparm: a parameter array overflowed
>
> (e.g. the table of dihedral params)
> NUMBND = 105 max is 5000
> NUMANG = 221 max is 900
> NPTRA = 404 max is 1200
> NATYP = 67 max is 100
> NPHB = 0 max is 200
> NTTYP = 2278 max is 1830
>
>
> The NTTYP value exceed the max. I thought the problem can be solved by
> upgrading to amber 12 as suggested ....
>
This max value has not changed since 2005, as this issue has never come up
before. As an example, I have a topology file with a pure protein in
explicit solvent (~20K total atoms), and NTYPES has a value of 16, which is
far fewer than the 60 allowable nonbonded atom types (60*(60+1)/2 == 1830).
Even a combined system that has lipids, amino acids, and carbohydrates
surrounded by explicit solvent should probably have fewer than 60 atom
types unless you modified the topology file somehow. Your topology file
has 67 atom types (67*(67+1)/2 == 2278).
It is possible that chamber is not condensing the atom types as much as
possible, but I'm not familiar enough with that code to determine for sure.
Your only recourse in this situation is to modify the maximum value (1830)
and push it up to 2278 or higher to avoid this issue. Luckily, the
constant "1830" is only present in the source code for this particular use,
so you can simply do a grep for 1830 and universally replace it with 2278
to fix your problem (don't forget to recompile afterwards). (The files you
should be modifying are parms.F90 and rdparm.F90 in $AMBERHOME/src/sander).
If you plan to use sander.MPI, though, you will also have to change the
value of BC_PARMR from 24560 to the sum of all array lengths in the rparms
common block. (It's actually incorrect right now, it should be 30050 in
order for the 'new vdw model' to work in parallel).
Good luck,
Jason
> >From this link http://archive.ambermd.org/201211/0137.html it was
> suggested to change the value in parms.F90 and rdparm.F90, but i'm
> reluctant to do so.
>
> May i know what is the real problem behind and is there any other
> workaround for this problem?
>
The problem is that you have too many non-bonded atom types. The value of
nttyp is NTYPES*(NTYPES+1)/2, where NTYPES is one of the prmtop pointers
(using the printPointers command in xparmed.py or parmed.py will print out
the value of all of the POINTERS for you). You have 67 different atom types
>
>
> Thanks and regards,
> Colvin
>
> On 6/7/12, colvin <colvin4367.gmail.com> wrote:
> > Thank you very much for your reply. We are currently using Amber10.
> > Thanks again!
> >
> > On Wed, Jun 6, 2012 at 7:53 PM, Bill Miller III <brmilleriii.gmail.com>
> > wrote:
> >> I believe these are two different issues, and have nothing to do with
> >> your
> >> prmtop files. The PB error is something that was recently reported here:
> >> http://archive.ambermd.org/201205/0591.html. MMPBSA.py uses the new
> >> dec_verbose control variable in its PB input, but this variable was not
> >> introduced into sander until Amber12. Since you don't have sander from
> >> Amber 12, then your sander executable cannot read this input variable.
> >> You
> >> should be able to remove the dec_verbose variable from the
> MMPBSA_pb.mdin
> >> file and then re-run the MMPBSA.py command line with the -use-mdins flag
> >> at
> >> the end. This should work for your PB calculation.
> >>
> >> For decomposition analysis, what version of Amber (sander) do you have?
> >> Decomposition analysis with MMPBSA.py only works with Amber 11 and newer
> >> releases. Your sander output file says Amber 10 at the top. If that is
> >> correct, then you will not be able to get reliable results for
> >> decomposition analysis with MMPBSA.py unless you upgrade to Amber 11 or
> >> Amber 12.
> >>
> >> I hope that helps.
> >>
> >> -Bill
> >>
> >> On Wed, Jun 6, 2012 at 4:49 AM, colvin <colvin4367.gmail.com> wrote:
> >>
> >>> Dear all,
> >>>
> >>> I'm using MMPBSA.py in Ambertools12 for free energy binding
> >>> calculations. I use cpptraj to generate separate prmtop files
> >>> (complex.prmtop, rec.prmtop and lig.prmtop) by stripping different
> >>> parts of the trajectory. FYI, my original prmtop file used for MD runs
> >>> is from CHAMBER.
> >>>
> >>> For GB and nmode parts, the calculations were done successfully but
> >>> for PB and decomp, the program ended with the error:
> >>>
> >>> CalcError: /usr/local/amber12/bin/mmpbsa_py_energy failed with prmtop
> >>> rec_lig.prmtop! (rec_lig.prmtop is my complex.prmtop)
> >>>
> >>> and this is the output from _MMPBSA_complex_pb.mdout.0
> >>>
> >>>
> >>> Reading parm file (rec_lig.prmtop)
> >>> title:
> >>>
> >>> mm_options: e_debug=3
> >>> mm_options: ipb=2
> >>> mm_options: inp=2
> >>> mm_options: epsin=1.000000
> >>> mm_options: epsout=80.000000
> >>> mm_options: smoothopt=1
> >>> mm_options: istrng=0.000000
> >>> mm_options: radiopt=1
> >>> mm_options: dprob=1.400000
> >>> mm_options: iprob=2.000000
> >>> mm_options: npbopt=0
> >>> mm_options: solvopt=1
> >>> mm_options: accept=0.001000
> >>> mm_options: maxitn=1000
> >>> mm_options: fillratio=4.000000
> >>> mm_options: space=0.500000
> >>> mm_options: nfocus=2
> >>> mm_options: fscale=8
> >>> mm_options: bcopt=5
> >>> mm_options: eneopt=2
> >>> mm_options: cutnb=0.000000
> >>> mm_options: sprob=0.557000
> >>> mm_options: cavity_surften=0.037800
> >>> mm_options: cavity_offset=-0.569200
> >>> Processing ASCII trajectory (_MMPBSA_complex.mdcrd.0)
> >>>
> >>> Processing frame 1
> >>> iter Total bad vdW elect nonpolar EPB
> >>> frms
> >>> eff.c(2660) enb14 --> 1875.427
> >>> eff.c(2661) eel14 --> 8737.616
> >>>
> >>>
> >>>
> >>>
> >>> i then try to set used_sander=1, program ended with the same error and
> >>> output file:
> >>>
> >>>
> >>> -------------------------------------------------------
> >>> Amber 10 SANDER 2008
> >>> -------------------------------------------------------
> >>>
> >>> | Run on 06/06/2012 at 16:17:18
> >>> [-O]verwriting output
> >>>
> >>> File Assignments:
> >>> | MDIN: _MMPBSA_pb.mdin
> >>> | MDOUT: _MMPBSA_complex_pb.mdout.0
> >>> |INPCRD: _MMPBSA_dummycomplex.inpcrd.1
> >>> | PARM: rec_lig.prmtop
> >>> |RESTRT: _MMPBSA_restrt.0
> >>> | REFC: refc
> >>> | MDVEL: mdvel
> >>> | MDEN: mden
> >>> | MDCRD: mdcrd
> >>> |MDINFO: mdinfo
> >>> |INPDIP: inpdip
> >>> |RSTDIP: rstdip
> >>>
> >>> |INPTRA: _MMPBSA_complex.mdcrd.0
> >>> |
> >>>
> >>> Here is the input file:
> >>>
> >>> File generated by MMPBSA.py
> >>> &cntrl
> >>> nsnb=99999, dec_verbose=0, ipb=2,
> >>> ntb=0, cut=999.0, imin=5, inp=2,
> >>> igb=10,
> >>> /
> >>> &pb
> >>> maxitn=1000, fillratio=4.0, radiopt=1,
> >>> /
> >>> error in reading namelist cntrl
> >>>
> >>>
> >>>
> >>> For decomp, the program ended with the same error as well, with the
> >>> output:
> >>>
> >>> -------------------------------------------------------
> >>> Amber 10 SANDER 2008
> >>> -------------------------------------------------------
> >>>
> >>> | Run on 06/06/2012 at 16:12:12
> >>> [-O]verwriting output
> >>>
> >>> File Assignments:
> >>> | MDIN: _MMPBSA_gb_decomp_com.mdin
> >>> | MDOUT: _MMPBSA_complex_gb.mdout.0
> >>> |INPCRD: _MMPBSA_dummycomplex.inpcrd.1
> >>> | PARM: rec_lig.prmtop
> >>> |RESTRT: _MMPBSA_restrt.0
> >>> | REFC: refc
> >>> | MDVEL: mdvel
> >>> | MDEN: mden
> >>> | MDCRD: mdcrd
> >>> |MDINFO: mdinfo
> >>> |INPDIP: inpdip
> >>> |RSTDIP: rstdip
> >>>
> >>> |INPTRA: _MMPBSA_complex.mdcrd.0
> >>> |
> >>>
> >>> Here is the input file:
> >>>
> >>> File generated by MMPBSA.py
> >>> &cntrl
> >>> nsnb=99999, ntb=0, surften=0.0072,
> >>> extdiel=80.0, ncyc=0, cut=999.0,
> >>> gbsa=2, saltcon=0.15, imin=5,
> >>> idecomp=2, igb=5,
> >>> /
> >>> Residues considered as REC
> >>> RRES 1 264
> >>> END
> >>> Residues considered as LIG
> >>> LRES 265 265
> >>> END
> >>> Residues to print
> >>> RES 1 265
> >>> END
> >>> END
> >>>
> >>>
> >>>
> --------------------------------------------------------------------------------
> >>> 1. RESOURCE USE:
> >>>
> >>>
> --------------------------------------------------------------------------------
> >>>
> >>> | Flags:
> >>> | New format PARM file being parsed.
> >>> | Version = 1.000 Date = 06/04/12 Time = 16:08:54
> >>> NATOM = 4304 NTYPES = 67 NBONH = 2175 MBONA = 2188
> >>> NTHETH = 4881 MTHETA = 2995 NPHIH = 8137 MPHIA = 3894
> >>> NHPARM = 0 NPARM = 0 NNB = 23795 NRES = 265
> >>> NBONA = 2188 NTHETA = 2995 NPHIA = 3894 NUMBND = 105
> >>> NUMANG = 221 NPTRA = 404 NATYP = 67 NPHB = 0
> >>> IFBOX = 0 NMXRS = 26 IFCAP = 0 NEXTRA = 0
> >>> NCOPY = 0
> >>>
> >>>
> >>> rdparm: a parameter array overflowed
> >>>
> >>> (e.g. the table of dihedral params)
> >>> NUMBND = 105 max is 5000
> >>> NUMANG = 221 max is 900
> >>> NPTRA = 404 max is 1200
> >>> NATYP = 67 max is 100
> >>> NPHB = 0 max is 200
> >>> NTTYP = 2278 max is 1830
> >>>
> >>>
> >>>
> >>> I'm not sure what is the problem with my complex.prmtop, and why GB
> >>> and nmode calculations can be done with the same prmtop file but not
> >>> the PB and decomp.
> >>>
> >>> Pls advise.
> >>>
> >>> Thanks and regards,
> >>> colvin
> >>>
> >>> _______________________________________________
> >>> 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
> >> 352-392-6715
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
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> >
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Nov 27 2012 - 05:00:04 PST
