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
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Wed Jun 06 2012 - 05:00:02 PDT
