Did you see any error messages anywhere?
On Mon, Jul 9, 2012 at 8:25 AM, <rajeevy.iitk.ac.in> wrote:
> Thanks Jason for your reply,
> Now i m using Ubuntu, and test for ambertools12 was completed.
> However I met to a problem, when running PB calculation....
> here is the command line and messege..........
> *************************
> rajeev.RAJ:~/hsa_c152$ $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o
> FINAL_RESULTS_MMPBSA.dat -sp hsa_c152.prmtop -cp hsa_c152_vac.prmtop -rp
> hsa_vac.prmtop -lp c152_vac.prmtop -y *.mdcrd
>
> Reading command-line arguments and input files...
> Loading and checking parameter files for compatibility...
> mmpbsa_py_energy found! Using
> /home/rajeev/local/amber12/bin/mmpbsa_py_energy
> cpptraj found! Using /home/rajeev/local/amber12/bin/cpptraj
> Preparing trajectories for simulation...
> 400 frames were processed by cpptraj for use in calculation.
>
> Beginning GB calculations with
> /home/rajeev/local/amber12/bin/mmpbsa_py_energy
> calculating complex contribution...
>
> calculating receptor contribution...
> calculating ligand contribution...
>
> Beginning PB calculations with
> /home/rajeev/local/amber12/bin/mmpbsa_py_energy
> calculating complex contribution...
> CalcError: /home/rajeev/local/amber12/bin/mmpbsa_py_energy failed with
> prmtop hsa_c152_vac.prmtop!
> Exiting. All files have been retained.
>
> and the output file for PB calculations
> is......(_MMPBSA_complex_pb.mdout.0)
>
> --------------------------------------------------------------------------------
> Reading parm file (hsa_c154_vac.prmtop)
> title:
>
> 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=150.000000
> 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
> eff.c(2660) enb14 --> 1925.800
>
> Thanks
> Rajeev
>
>
>
>
> > The SUSE package manager is zypper. You will need to run a command like:
> >
> > sudo zypper install patch
> >
> > Note this is not the only package you will need to install. You will
> also
> > need the packages gcc, gcc-c++, gcc-fortran, libtool, xorg-x11-devel,
> > xorg-x11-libXt-devel, libbz2-devel, autoconf, and automake if you don't
> > already have those packages installed.
> >
> > HTH,
> > Jason
> >
> > On Wed, Jul 4, 2012 at 10:54 AM, <rajeevy.iitk.ac.in> wrote:
> >
> >> dear ...dac,
> >> Thank you for ur reply
> >> For i m using OpenSuse 11.3, for this which patch programm i should use
> >>
> >> Thanks
> >> Rajeev
> >>
> >> > On Wed, Jul 04, 2012, rajeevy.iitk.ac.in wrote:
> >> >>
> >> >> Applying AmberTools12 patches
> >> >> Fatal Error: Cannot find the patch program.
> >> >
> >> > You need to install the patch program; exactly how depends on what OS
> >> you
> >> > are
> >> > using:
> >> >
> >> > sudo apt-get install patch (for Debian/Ubuntu Linux)
> >> > sudo yum install patch (for Fedora and similar)
> >> > sudo port install patch (for MacOS using macports)
> >> >
> >> > otherwise, checkout http://en.wikipedia.org/wiki/Patch_(Unix).
> >> >
> >> > [In the latest version Ubuntu appears to have dropped patch as
> >> something
> >> > you always get; I'll update the web page about this.]
> >> >
> >> > ....dac
> >> >
> >> >
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >>
> >>
> >> _______________________________________________
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> >> 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
> >
>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Jul 09 2012 - 09:00:02 PDT
