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
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Received on Wed Mar 27 2013 - 14:30:02 PDT
