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
>
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Received on Thu Dec 15 2011 - 13:00:03 PST
