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
> > _______________________________________________
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>
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Received on Fri Aug 16 2019 - 05:30:01 PDT
