It works! Thank you so much!
Best regards,
Marina
Citiram Ray Luo <ray.luo.uci.edu>:
> 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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>>>
>>
>>
>>
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Received on Mon Feb 15 2010 - 05:00:02 PST
