Thank you Jason. I already changed the value accordingly but i'm not quite
sure what do you mean about "change the
value of BC_PARMR from 24560 to the sum of all array lengths in the
rparms common block". Im sorry, could you pls explain more? Many thanks.
On Tue, Nov 27, 2012 at 8:54 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> 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 - 22:00:02 PST
