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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Received on Thu Feb 11 2010 - 09:30:02 PST
