You're running a decomposition analysis with MMPBSA.py, but not with
mm_pbsa.pl. Decomposition adds significant time to the calculation
(especially for PB, I believe).
HTH,
Jason
On Thu, Dec 15, 2011 at 3:44 PM, Qinghua Liao <fantasticqhl.gmail.com>wrote:
> Dear Jason,
>
> Thanks again. Here is my input file for the mm_pbsa.pl calculation:
>
> .GENERAL
> #
> VERBOSE 0
> PARALLEL 8
> #
> PREFIX snapshot
> PATH ../snapshots/
> START 1
> STOP 400
> OFFSET 1
> #
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> #
> COMPT ../com.prmtop
> RECPT ../rec.prmtop
> LIGPT ../lig.prmtop
> #
> GC 0
> AS 0
> DC 0
> #
> MM 1
> GB 1
> PB 1
> MS 1
> #
> NM 0
> #
>
> ################################################################################
> .PB
> #
> PROC 2
> REFE 0
> INDI 1.0
> EXDI 80.0
> SCALE 2
> LINIT 1000
> PRBRAD 1.4
> ISTRNG 0.10
> RADIOPT 1
> INP 1
> #
> SURFTEN 0.00542
> SURFOFF -1.008
> #
> IVCAP 0
> CUTCAP -1.0
> XCAP 0.0
> YCAP 0.0
> ZCAP 0.0
> #
>
> ################################################################################
> .MM
> #
> DIELC 1.0
> #
>
> ################################################################################
> .GB
> #
> #
> IGB 5
> GBSA 2
> SALTCON 0.10
> EXTDIEL 80.0
> INTDIEL 1.0
> #
> SURFTEN 0.0072
> SURFOFF 0.00
> #
>
> ################################################################################
> .MS
> #
> #
> PROBE 0.0
> #
>
> ################################################################################
> .PROGRAMS
> #
> # Additional program executables can be defined here
> #
> #
>
> ################################################################################
>
> How should I check the temporary files? In mm_pbsa.pl's calculation, I can
> check the output files for the process, but in the python version, how
> should I checnk the process?
>
> Right now, I guess that the calculation was died, however, the sander are
> still working. Is it possible for the python version?
> Here are the temporary files in the working folder:
>
> _MMPBSA_avgcomplex.pdb _MMPBSA_comtraj.in.0
> _MMPBSA_ligandinpcrd.in _MMPBSA_pb_decomp_rec.mdin
> _MMPBSA_ptraj5.out _MMPBSA_receptor.pdb
> _MMPBSA_cenptraj.in _MMPBSA_dummycomplex.inpcrd.1
> _MMPBSA_ligand.mdcrd _MMPBSA_ptraj1.out
> _MMPBSA_ptraj6.out _MMPBSA_rectraj.in
> _MMPBSA_complex_gb.mdout.0 _MMPBSA_dummyligand.inpcrd.1
> _MMPBSA_ligand.mdcrd.0 _MMPBSA_ptraj1.out.0 mmpbsa_py.in
> _MMPBSA_rectraj.in.0
> _MMPBSA_complexinpcrd.in _MMPBSA_dummyreceptor.inpcrd.1
> _MMPBSA_ligand.pdb _MMPBSA_ptraj2.out
> _MMPBSA_receptor_gb.mdout.0 _MMPBSA_.restrt.0
> _MMPBSA_complex.mdcrd _MMPBSA_gb_decomp_com.mdin
> _MMPBSA_ligtraj.in _MMPBSA_ptraj2.out.0
> _MMPBSA_receptorinpcrd.in mpd.hosts
> _MMPBSA_complex.mdcrd.0 _MMPBSA_gb_decomp_lig.mdin
> _MMPBSA_ligtraj.in.0 _MMPBSA_ptraj3.out
> _MMPBSA_receptor.mdcrd nohup.out
> _MMPBSA_complex_pb.mdout.0 _MMPBSA_gb_decomp_rec.mdin
> _MMPBSA_pb_decomp_com.mdin _MMPBSA_ptraj3.out.0
> _MMPBSA_receptor.mdcrd.0
> _MMPBSA_complex.pdb _MMPBSA_ligand_gb.mdout.0
> _MMPBSA_pb_decomp_lig.mdin _MMPBSA_ptraj4.out
> _MMPBSA_receptor_pb.mdout.0
>
>
> It seems no change for sometime now. I am going to kill one and redo it.
> Thanks!
>
>
> Best Regards,
>
> Qinghua
>
>
>
> On Thu, Dec 15, 2011 at 7:50 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > What was your mm_pbsa.pl input file? Are temporary files (_MMPBSA_*)
> > still
> > being written to for MMPBSA.py?
> >
> > On Thu, Dec 15, 2011 at 11:21 AM, Qinghua Liao <fantasticqhl.gmail.com
> > >wrote:
> >
> > > Dear amber users,
> > >
> > > Is it very slow for calculating binding energy and decomposition
> > > simultaneously? It has been more than 24 hours for the calculation
> using
> > 16
> > > cores' MMPBSA.MPI, and it has already finished using 8 core's
> > > mm_pbsa.plfor the calculation of binding energy. Here is the input
> > > file:
> > >
> > > &general
> > > startframe=1, endframe=400, interval=1,
> > > verbose=1, keep_files=1,
> > > /
> > > &gb
> > > igb=5, saltcon=0.10, surften=0.0072, surfoff=0.00,
> > > /
> > > &pb
> > > indi=1.0, exdi=80.0, scale=2.0, linit=1000, prbrad=1.4,
> > > inp=1, istrng=0.10, cavity_surften=0.00542, cavity_offset=-1.008,
> > > fillratio=4.0,
> > > /
> > > &decomp
> > > idecomp=2, dec_verbose=3,
> > > /
> > >
> > > I guess that there may be some problem with my input file, could
> someone
> > > give me a suggestion? Thanks very much!
> > >
> > > --
> > > Best Regards,
> > >
> > > Qinghua
> > > _______________________________________________
> > > 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
> >
> _______________________________________________
> 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
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Received on Thu Dec 15 2011 - 14:00:03 PST
