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
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Received on Thu Aug 16 2012 - 09:00:04 PDT
