Re: [AMBER] how to predict time for MMPBSA decomp analysis

From: vaibhav dixit <vaibhavadixit.gmail.com>
Date: Wed, 10 Oct 2012 11:55:06 +0530

Dear Dr. Jason, Soumya, and Amber community member,
Thanks for your suggestions. While revisiting this problem I have carefully
check all the output files. In one file _MMPBSA_complex_gb.mdout.0 I'm
getting the following output at the last in addition to other things, but
the job never seems to end. Top command shows that MMPBSA.py is still
running.

--------------------------
                    PRINT DECOMP - TOTAL ENERGIES

    resid |internal |vdw |eel |pol |sas
============================================================
TDC 267 19.029 -7.107 -20.431 -3.734 29.298
----------------
Does it mean that the jobs has completed but somehow failed to quit at the
last moment. As I'm not a programming expert so I can't guess whats really
happening here.

Command that I gave:
 $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa_decomp.in -o results_gb.dat -do
results_decom.dat -cp ../2PRG_RGZ_VAC.prmtop -rp ../2PRG_RGZ_prot.prmtop
-lp ../2PRG_RGZ_lig.prmtop -y ../2PRG_RGZ_md_100ns_VAC.mdcrd

MMPBSA input file:
---------------
Sample input file for GB and PB 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", dec_verbose=2
/
------------------
List of output files generated.
-rw-r--r-- 1 gncp users 177 Oct 10 11:32 mmpbsa_only_decomp.in
-rw-r--r-- 1 gncp users 303 Oct 10 11:33 _MMPBSA_gb_decomp_com.mdin
-rw-r--r-- 1 gncp users 258 Oct 10 11:33 _MMPBSA_gb_decomp_rec.mdin
-rw-r--r-- 1 gncp users 248 Oct 10 11:33 _MMPBSA_gb_decomp_lig.mdin
-rw-r--r-- 1 gncp users 163111 Oct 10 11:33 _MMPBSA_dummycomplex.inpcrd
-rw-r--r-- 1 gncp users 161505 Oct 10 11:33 _MMPBSA_dummyreceptor.inpcrd
-rw-r--r-- 1 gncp users 1708 Oct 10 11:33 _MMPBSA_dummyligand.inpcrd
-rw-r--r-- 1 gncp users 358189 Oct 10 11:33 _MMPBSA_receptor.pdb
-rw-r--r-- 1 gncp users 322446 Oct 10 11:33 _MMPBSA_receptor.mdcrd.0
-rw-r--r-- 1 gncp users 3571 Oct 10 11:33 _MMPBSA_ligand.pdb
-rw-r--r-- 1 gncp users 3291 Oct 10 11:33 _MMPBSA_ligand.mdcrd.0
-rw-r--r-- 1 gncp users 361753 Oct 10 11:33 _MMPBSA_complex.pdb
-rw-r--r-- 1 gncp users 325653 Oct 10 11:33 _MMPBSA_complex.mdcrd.0
-rw-r--r-- 1 gncp users 6024 Oct 10 11:33 _MMPBSA_normal_traj_cpptraj.out
-rw-r--r-- 1 gncp users 156511 Oct 10 11:34 _MMPBSA_complex_gb.mdout.0
-rw-r--r-- 1 gncp users 154702 Oct 10 11:35 _MMPBSA_receptor_gb.mdout.0
-rw-r--r-- 1 gncp users 1617 Oct 10 11:35 _MMPBSA_restrt.0
-rw-r--r-- 1 gncp users 14578 Oct 10 11:35 _MMPBSA_ligand_gb.mdout.0
drwxr-xr-x 2 gncp users 4096 Oct 10 11:35 .
-rw-r--r-- 1 gncp users 2832 Oct 10 11:35 _MMPBSA_info
-rw-r--r-- 1 gncp users 5664 Oct 10 11:35 results_gb.dat
-rw-r--r-- 1 gncp users 35 Oct 10 11:35 results_decom.dat
---------------

Thanks for your time and suggestions.


On Tue, Aug 21, 2012 at 11:27 AM, Soumya Lipsa Rath <soumyalipsabt.gmail.com
> wrote:

> 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
> >
> _______________________________________________
> 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 Tue Oct 09 2012 - 23:30:04 PDT
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