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
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Received on Wed Jun 06 2012 - 20:30:03 PDT
