It seems that you have 40 snapshots, but the "com.all.out" file contains
multiple previous trial runs with one or two snapshots. You need to
completely clean up the working folder before starting a new job. The
script would keep append at the end of the .out file. This will screw up
the later statistics analysis.
All the best,
Ray
==========================================
Ray Luo, Ph.D.
Associate Professor in Computational
Biochemistry and Molecular Biophysics
Dept of Molecular Biology and Biochemistry
Dept of Biomedical Engineering
University of California, Irvine, CA 92697-3900
Email: rluo.uci.edu Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/rayl/
==========================================
Marina Grabar wrote:
> Yes, of course. Please find the files attached.
>
> Thank you,
> Marina
>
> Citiram Ray Luo <ray.luo.uci.edu>:
>
>> Can we look at your .out files produced by the script?
>>
>> Ray
>>
>> ==========================================
>> Ray Luo, Ph.D.
>> Associate Professor in Computational
>> Biochemistry and Molecular Biophysics
>> Dept of Molecular Biology and Biochemistry Dept of Biomedical
>> Engineering
>> University of California, Irvine, CA 92697-3900
>> Email: rluo.uci.edu Phones: (949) 824-9528, 9562
>> Web: http://rayl0.bio.uci.edu/rayl/
>> ==========================================
>>
>>
>>
>> Marina Grabar wrote:
>>> I'm using mm, gb, pb and ms... This is my input:
>>>
>>> .GENERAL
>>> PREFIX snapshot_DNA_TD22_2
>>> PATH ../extract_coords-II
>>> #
>>> COMPLEX 1
>>> RECEPTOR 1
>>> LIGAND 1
>>> #
>>> COMPT ../DNA_TD22_2_bv.top
>>> RECPT ../DNAzaTD22_2_bv.top
>>> LIGPT ../TD22_2_bv.top
>>> #
>>> GC 0
>>> AS 0
>>> DC 0
>>> #
>>> MM 1
>>> GB 1
>>> PB 1
>>> MS 1
>>> #
>>> NM 0
>>> #
>>> .PB
>>> #
>>> PROC 2
>>> REFE 0
>>> INDI 1.0
>>> EXDI 80.0
>>> SCALE 2
>>> LINIT 1000
>>> PRBRAD 1.4
>>> ISTRNG 0.0
>>> RADIOPT 0
>>> NPOPT 1
>>> CAVITY_SURFTEN 0.0072
>>> CAVITY_OFFSET 0.00
>>> #
>>> PB_SURFTEN 0.0072
>>> PB_SURFOFF 0.00
>>> #
>>> .MM
>>> #
>>> DIELC 1.0
>>> #
>>> .GB
>>> #
>>> IGB 2
>>> GBSA 1
>>> SALTCON 0.00
>>> EXTDIEL 80.0
>>> INTDIEL 1.0
>>> #
>>> SURFTEN 0.0072
>>> SURFOFF 0.00
>>> #
>>> .MS
>>> #
>>> PROBE 0.0
>>> #
>>> .PROGRAMS
>>> #
>>>
>>> Citiram Dwight McGee <dwight.mcgee.gmail.com>:
>>>
>>>> Which function of mm_pbsa.pl are you using, for example, gb, pb?
>>>>
>>>> On Thu, Feb 11, 2010 at 9:51 AM, Marina Grabar
>>>> <Marina.Grabar.irb.hr> wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> I'm trying to calculate free energies of binding (for complex
>>>>> between DNA
>>>>> and small molecule) with MM_PBSA method. I run the following
>>>>> command: "
>>>>> mm_pbsa.pl mm_pbsa_Binding.in > mm_pbsa_Binding.log" and after few
>>>>> minutes
>>>>> I got the message: "No data for 0+1 MM BOND 480". In my new log
>>>>> file there
>>>>> is no final part for statistics. I also tried to run
>>>>> mm_pbsa_statistics.pl(because it produced three intermediate files:
>>>>> snapshot_DNA_TD22_2_com.all.out, snapshot_DNA_TD22_2_rec.all.out and
>>>>> snapshot_DNA_TD22_2_lig.all.out) but after running it I became:
>>>>> =>> Reading input
>>>>> =>> Reordering files
>>>>> Final order:
>>>>> 1. snapshot_DNA_TD22_2_com.all.out: -
>>>>> 2. snapshot_DNA_TD22_2_rec.all.out: -
>>>>> 3. snapshot_DNA_TD22_2_lig.all.out: -
>>>>> =>> Reading files
>>>>> =>> Values of parameters
>>>>> TEMP = 300
>>>>> R = 8.314
>>>>> =>> Treat special parameters
>>>>> =>> Calc missing parameters
>>>>> =>> Calc average and stddev
>>>>> =>> Print output (decomp) to snapshot_DNA_TD22_2_statistics.out
>>>>> snapshot_DNA_TD22_2_statistics.out not opened
>>>>>
>>>>> ...and, of course, no statistics output file.
>>>>>
>>>>> Btw, we installed Amber 10 just few days ago and patched the
>>>>> latest version
>>>>> of bug fixes.
>>>>>
>>>>> I would be very grateful if anyone could help me to fix this
>>>>> problem...
>>>>>
>>>>> Best regards,
>>>>> Marina
>>>>>
>>>>> --
>>>>> Marina Grabar, B.Sc.
>>>>> Institute Rudjer Boskovic
>>>>> Bijenicka 54
>>>>> HR-10000, Zagreb
>>>>> CROATIA
>>>>> tel +385-1-4561025
>>>>> fax +385-1-4680245
>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> T. Dwight McGee Jr.
>>>> Quantum Theory Project
>>>> University of Florida
>>>> dwight.mcgee.gmail.com
>>>>
>>>> "Problems cannot be solved at the same level of awareness that created
>>>> them."
>>>> Albert Einstein
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>>
>>>
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
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Received on Fri Feb 12 2010 - 10:00:02 PST
