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
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Aug 16 2012 - 08:00:06 PDT
