Yes. MMPBSA.py is part of ambertools and is freely available without
amber19 license.
On Friday, August 16, 2019, shivangi agarwal <shiviagarwalpharma.gmail.com>
wrote:
> I don't have Amber latest package. But I have installed AmberTools19. Can
> it be run on AmberTools19?
>
> On Fri, Aug 16, 2019 at 2:58 PM Ray Luo <rluo.uci.edu> wrote:
>
> > Hi Shivangi,
> >
> > My guess is this is one of those errors due to the default radiopt=1
> > in the older amber releases ... Why not use amber18 or amber19
> > instead?
> >
> > All the best,
> > Ray
> > --
> > Ray Luo, Ph.D.
> > Professor of Structural Biology/Biochemistry/Biophysics,
> > Chemical Physics, Biomedical Engineering, and Chemical Engineering
> > Department of Molecular Biology and Biochemistry
> > University of California, Irvine, CA 92697-3900
> >
> > On Fri, Aug 16, 2019 at 4:23 PM shivangi agarwal
> > <shiviagarwalpharma.gmail.com> wrote:
> > >
> > > Hello all
> > >
> > > I want to calculate MMGBSA from dcd file. I have converted it to .mdcrd
> > > using cpptraj.
> > >
> > > cpptraj -p complex-box.prmtop -y sim1_14.dcd -x sim1_14_complex.mdcrd
> > > Then using,
> > >
> > > MMPBSA.py -i mmpbsa.in -o FINAL_RESULTS_MMPBSA_20_frames.dat -sp
> > > complex-box.prmtop -cp complex.prmtop -rp receptor.prmtop -lp
> > ligand.prmtop
> > > -y sim1_14_complex.mdcrd
> > >
> > > ###MMPBSA.in#############
> > >
> > > Input file for running PB and GB in serial
> > > &general
> > > endframe=20, keep_files=2,
> > > /
> > > &gb
> > > igb=2, saltcon=0.100,
> > > /
> > > &pb
> > > istrng=0.100,
> > > /
> > > ################################
> > >
> > > But getting error,
> > >
> > > Reading command-line arguments and input files...
> > > Loading and checking parameter files for compatibility...
> > > mmpbsa_py_energy found! Using
> > /opt/apps/amber/amber12/bin/mmpbsa_py_energy
> > > cpptraj found! Using /opt/apps/amber/amber12/bin/cpptraj
> > > Preparing trajectories for simulation...
> > > 20 frames were processed by cpptraj for use in calculation.
> > >
> > > Beginning GB calculations with
> > /opt/apps/amber/amber12/bin/mmpbsa_py_energy
> > > calculating complex contribution...
> > > calculating receptor contribution...
> > > calculating ligand contribution...
> > >
> > > Beginning PB calculations with
> > /opt/apps/amber/amber12/bin/mmpbsa_py_energy
> > > calculating complex contribution...
> > > CalcError: /opt/apps/amber/amber12/bin/mmpbsa_py_energy failed with
> > prmtop
> > > complex.prmtop!
> > > Exiting. All files have been retained.
> > >
> > > Can someone suggest?
> > >
> > > Regards
> > > Shivangi Agarwal
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
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> >
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--
Best Regards
Elvis Martis
Mumbai.
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Received on Fri Aug 16 2019 - 05:30:02 PDT
