Ahoj Michale,
no protoze Koca tvrdil, ze to ma byt "obecne" (i kdyz pochybuju,
ze na tuhle sekci nekdo obecny zamiri) tak budu mluvit pouze
o flexibilite rRNA segmentu, zadny overlap nehrozi.
To uz bych se davno ozval.
Mozna Te ale poprosim o nejake slidy, budu mit na tema
ribozymy prednasku v Italii.
Vis, kde to je? Ja z toho planku nebyl moudry.....
Ale ja se ztratim vsude.
Tyhle akce nam byl cert dluznej, stoji to spoustu casu...
Mej se Jirka
On Tue, 21 Aug 2012, vaibhav dixit wrote:
> Date: Tue, 21 Aug 2012 10:33:13 +0530
> From: vaibhav dixit <vaibhavadixit.gmail.com>
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] how to predict time for MMPBSA decomp analysis
>
> Dear Amber community members,
> I have resubmitted an MMPBSA decomp job with only one residue and 3
> tarjectories.
> But that also seems to have fallen in some loop and is running for more
> than 2 days.
>
> I have provided other details for "make test" in an earlier mail (see
> below).
> Please suggest me a remedy for this issue with MMPBSA and decomp job.
>
> Thank you.
>
> On Thu, Aug 16, 2012 at 9:29 PM, vaibhav dixit <vaibhavadixit.gmail.com>wrote:
>
>> Dear Dr. Jason and amber community members,
>> Thanks for your reply.
>> I am using Amber 12 version and AmberTools12.
>>
>> I had earlier put a query about amber make test on the same installation
>> here. http://archive.ambermd.org/201208/0019.html
>> Please let me know if more information is needed to understand this
>> problem.
>> Thank you.
>>
>> On Thu, Aug 16, 2012 at 8:04 PM, Jason Swails <jason.swails.gmail.com>wrote:
>>
>>> On Thu, Aug 16, 2012 at 1:45 AM, vaibhav dixit <vaibhavadixit.gmail.com
>>>> wrote:
>>>
>>>> Dear Amber community members,
>>>> I have 100ns MD trajectories for a protein-ligand complex with around
>>> 276
>>>> residues.
>>>> I have submitted the following job for MMPBSA and decomposition
>>> analysis.
>>>> Only 3 frames were included in this trial job with 8 AAs for which
>>> decomp
>>>> analysis was requested.
>>>> The GB analysis is finished quickly but decomposition analysis is
>>> running
>>>> for more than three days.
>>>> How can I monitor the status of the job? when it is likely to finish? Is
>>>> there something wrong in the input structure/command? Will running the
>>> job
>>>> in parallel help?
>>>>
>>>> I have used the following command.
>>>>
>>>> $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa_decomp.in -o results_decomp.dat
>>> -do
>>>> FINAL_DECOMP_MMPBSA.dat -cp complex_VAC.prmtop -rp protein.prmtop -lp
>>>> lig.prmtop -y 100ns_VAC.mdcrd
>>>>
>>>
>>> The GB decomp analysis should not take that long. It will take a little
>>> longer than normal GB (and a bit longer still for pairwise decomposition).
>>> If you have only 1 CPU, there's no benefit to running in parallel (unless
>>> that CPU has multiple cores or has hyperthreading).
>>>
>>> What version of Amber and AmberTools are you using? (It appears to be
>>> AmberTools 12, but what about Amber?)
>>>
>>> Lastly, do the MMPBSA.py decomp tests pass?
>>>
>>> Thanks!
>>> Jason
>>>
>>>
>>>>
>>>> I'm using a Opensuse 12.01 system with 4GB ram and 1 cpu.
>>>>
>>>> Input file: mmpbsa_decomp.in
>>>> ---------
>>>> Sample input file for GB and decomp calculation
>>>> &general
>>>> startframe=50, endframe=5000, interval=2000,
>>>> verbose=2, keep_files=0,
>>>> /
>>>> &gb
>>>> igb=5, saltcon=0.150,
>>>> /
>>>> &decomp
>>>> idecomp=2, print_res="267; 117; 243; 68; 83; 79; 80; 82", dec_verbose=3
>>>> /
>>>>
>>>> Thank you.
>>>> --
>>>> With regards
>>>>
>>>> Vaibhav A. Dixit
>>>> Ph.D. Scholar
>>>> Department of Medicinal Chemistry
>>>> Natl. Inst. Pharm. Edu. & Res. (NIPER)
>>>> Sector 67, Phase X, S.A.S. Nagar (Mohali)
>>>> Punjab -160 062 INDIA
>>>> Phone (Mobile): +919915214408
>>>> E-mail: vaibhavadixit.gmail.com
>>>> www.niper.nic.in
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>>
>>>
>>> --
>>> Jason M. Swails
>>> Quantum Theory Project,
>>> University of Florida
>>> Ph.D. Candidate
>>> 352-392-4032
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>>
>> --
>> With regards
>>
>> Vaibhav A. Dixit
>> Ph.D. Scholar
>> Department of Medicinal Chemistry
>> Natl. Inst. Pharm. Edu. & Res. (NIPER)
>> Sector 67, Phase X, S.A.S. Nagar (Mohali)
>> Punjab -160 062 INDIA
>> Phone (Mobile): +919915214408
>> E-mail: vaibhavadixit.gmail.com
>> www.niper.nic.in
>>
>
>
>
> --
> With regards
>
> Vaibhav A. Dixit
> Ph.D. Scholar
> Department of Medicinal Chemistry
> Natl. Inst. Pharm. Edu. & Res. (NIPER)
> Sector 67, Phase X, S.A.S. Nagar (Mohali)
> Punjab -160 062 INDIA
> Phone (Mobile): +919915214408
> E-mail: vaibhavadixit.gmail.com
> www.niper.nic.in
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Aug 21 2012 - 01:00:04 PDT
