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 ....
>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?
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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Received on Tue Nov 27 2012 - 01:30:03 PST
