okay, where can I find the files?
On Jul 9, 2012, at 6:09 PM, Ray Luo wrote:
> 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
>>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
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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
>>>> _______________________________________________
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>>>> 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 - 18:00:03 PDT
