Ya, but I am getting certain errors:
MMPBSA.py -i mmpbsa.in -o FINAL_RESULTS_MMPBSA_3.dat -sp complex-box.prmtop
-cp complex.prmtop -rp receptor.prmtop -lp ligand.prmtop -y
/media/ravi/data/MM_dcd/sim1_14_complex.mdcrd
Traceback (most recent call last):
File "/home/ravi/anaconda3/bin/MMPBSA.py", line 41, in <module>
from MMPBSA_mods import main
File
"/home/ravi/anaconda3/lib/python3.5/site-packages/MMPBSA_mods/main.py",
line 42, in <module>
from MMPBSA_mods.commandlineparser import parser
File
"/home/ravi/anaconda3/lib/python3.5/site-packages/MMPBSA_mods/commandlineparser.py",
line 61, in <module>
'spc.xvv'))
File "/home/ravi/anaconda3/lib/python3.5/posixpath.py", line 89, in join
genericpath._check_arg_types('join', a, *p)
File "/home/ravi/anaconda3/lib/python3.5/genericpath.py", line 143, in
_check_arg_types
(funcname, s.__class__.__name__)) from None
TypeError: join() argument must be str or bytes, not 'NoneType'
On Fri, Aug 16, 2019 at 5:47 PM Elvis Martis <elvis_bcp.elvismartis.in>
wrote:
> 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
> > >
> > > _______________________________________________
> > > 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
> >
>
>
> --
> Best Regards
> Elvis Martis
> Mumbai.
> _______________________________________________
> AMBER mailing list
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>
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Received on Fri Aug 16 2019 - 06:00:06 PDT
