It appears that *snapshot-2* has BOND= ************ *in the
snapshot_DNA_TD22_2_com.all.out *and that would certainly cause
mm_pbsa_statistics.pm to crash and give the error of "No data for 0+1 MM
BOND 480". Did you manually edit the com.all.out file because it is not the
same size as the lig and rec file and the frame numbers are out of order ?
As to why BOND=******* I am not certain it could be a couple of reasons but
I would suggest first going back and looking at the actual MD to see if
everything stable then just work from there.
Good luck
On Fri, Feb 12, 2010 at 6:57 AM, Marina Grabar <Marina.Grabar.irb.hr> 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
>>>>
>>>>
>>>
>>>
>>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
>
> --
> 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
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Received on Fri Feb 12 2010 - 07:30:03 PST
