Please apply the bugfix patches as Jason suggested, or just wait a few
weeks when the new AmberTools package is released.
All the best,
Ray
On Wed, Mar 27, 2013 at 2:01 PM, Chinthaka Ratnaweera <cnr88.msstate.edu> wrote:
> I actually followed the amber tutorials. Accordingly for pbsa calculation
> on protein-ligand complex they used GAFF-based prmtop for the ligand. Is
> this problem in amber12 only? Is there any otherway I can calculate pbsa
> energy?
> Thank you
> Chinthaka
>
> On Wed, Mar 27, 2013 at 1:02 PM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
>
>> 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
>>
>> _______________________________________________
>> 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 - 14:30:03 PDT
