Qin,
Can you try to reproduce the problem?
Ray Luo, Ph.D.
On Jul 9, 2012, at 10:43 AM, Jason Swails <jason.swails.gmail.com> wrote:
> 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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>>>>
>>>
>>>
>>>
>>> --
>>> 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 - 16:30:03 PDT
