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
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Jul 09 2012 - 05:30:02 PDT
