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
_______________________________________________
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http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 12 2010 - 04:00:03 PST
