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
>> >> >
>> >>
>> >>
>> >> _______________________________________________
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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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Jul 09 2012 - 22:00:02 PDT
