Hi,
Can u try running using dec_verbose value less than 3 because according to
the manual it consumes lot of memory.. But again it shouldn't take so
long.. also try putting a comma after dec_verbose and check.
Thanks
Soumya
On Tue, Aug 21, 2012 at 10:33 AM, vaibhav dixit <vaibhavadixit.gmail.com>wrote:
> 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 Mon Aug 20 2012 - 23:00:04 PDT
