Can you email Qin and me off the list an archive of the working folder
containing all the the files so we can see where it stopped?
All the best,
Ray
On Tue, Jul 10, 2012 at 12:40 AM, <rajeevy.iitk.ac.in> wrote:
> No, I didn't see any error message!!!!!!!
>
> > 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
> >> >> >
> >> >>
> >> >>
> >> >> _______________________________________________
> >> >> 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
> >> >
> >>
> >>
> >> _______________________________________________
> >> 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
> >
>
>
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Received on Tue Jul 10 2012 - 08:30:04 PDT
