Are you using GAFF-based prmtop files for your ligands? This is
probably the cause of what you are seeing here since you are
requesting the new nonpolar solvent model but the program does not
allow you to use it for GAFF-based prmtop files. In the next release,
we will lift the restriction of running the new solvent model (inp=2)
with all the new force field variations in Amber.
Ray
On Wed, Mar 27, 2013 at 10:46 AM, Chinthaka Ratnaweera
<cnr88.msstate.edu> wrote:
> Thank you
>
> This is only what is in the _MMPBSA_complex_pb.mdout.0. file. I don't see
> an error msg there.
>
> Reading parm file (../complex.prmtop)
> title:
> default_name
>
> 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=100.000000
> 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
>
>
>
> On Wed, Mar 27, 2013 at 11:48 AM, Jason Swails <jason.swails.gmail.com>wrote:
>
>> The error message will be found in _MMPBSA_complex_pb.mdout.0.
>>
>> If you google the error message you get, it should take you to previous
>> discussions on the mailing list where people have asked that question and
>> received answers.
>>
>> Good luck,
>> Jason
>>
>> On Wed, Mar 27, 2013 at 12:08 PM, Chinthaka Ratnaweera <cnr88.msstate.edu
>> >wrote:
>>
>> > Hi
>> > I am getting following error when calculating the MMPBSA energies with
>> > MMPBSA.py. But GBSA works fine. Error msg and input files are paste
>> below.
>> > Thank you in advanced.
>> >
>> > Reading command-line arguments and input files...
>> > Loading and checking parameter files for compatibility...
>> > mmpbsa_py_energy found! Using /usr/local/amber12/bin/mmpbsa_py_energy
>> > cpptraj found! Using /usr/local/amber12/bin/cpptraj
>> > Preparing trajectories for simulation...
>> > 50 frames were processed by cpptraj for use in calculation.
>> >
>> > Beginning PB calculations with /usr/local/amber12/bin/mmpbsa_py_energy
>> > calculating complex contribution...
>> > CalcError: /usr/local/amber12/bin/mmpbsa_py_energy failed with prmtop
>> > ../complex.prmtop!
>> >
>> >
>> > Exiting. All files have been retained.
>> >
>> > ...................
>> >
>> > input file
>> >
>> > input file for running PB and GB in serial
>> > &general
>> > endframe=50, keep_files=2,
>> > /
>> > &gb
>> > igb=2, saltcon=0.100,
>> > /
>> > &pb
>> > istrng=0.100,
>> > /
>> >
>> >
>> > --
>> > Chinthaka Nadun Ratnaweera
>> > Mississippi State University
>> > 310 Presidents Circle
>> > Starkville, MS 39762
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Candidate
>> 352-392-4032
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Chinthaka Nadun Ratnaweera
> Hand Lab Rm 1126
> Mississippi State University
> 310 Presidents Circle
> Starkville, MS 39762
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed Mar 27 2013 - 11:30:03 PDT
