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
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Received on Mon Aug 20 2012 - 22:30:04 PDT
