2011/9/30 Marek Maly <marek.maly.ujep.cz>
> Thanks ! I agree that #2 is not critical problem and in case of DELTA
> calculation,
> there will be probably almost zero influence of "use_sander". On the other
> hand
> #1 seems to me as serious problem. Would be also interesting to see/compare
> salt sensitivity in case of use APBS or Delphi instead native Amber PB
> solver.
>
You can already try APBS via the use of sander.APBS if you're really
interested (it may also be worth trying the non-linear PB). As for the
issue involving changing salt concentrations, the GB approximation for
including salt effects is rather crude (and indeed the PB results suggest
that salt concentration has no effect in that range statistically
speaking). The results are highly system-dependent, if I recall correctly,
and these effects appear to be artifacts of the GB model you chose. You can
try other models (like igb=8, which will forcibly use sander) to see if that
mediates the effect...
Other than those comments, I'd have to defer to the more experienced GBers
out there that may know what's happening better than I do. This falls in
the range of sander/pmemd/GB issues, though, and not so much in the
operation of either MM/PBSA script.
HTH,
Jason
>
> Let me/us know when you have some news regarding this issue.
>
> Best wishes,
>
> Marek
>
>
>
>
>
> Dne Fri, 30 Sep 2011 23:11:52 +0200 Jason Swails <jason.swails.gmail.com>
> napsal/-a:
>
> > It could be that some of the default parameters are different for
> > use_sander=0 and use_sander=1 (since the inputs are handled differently
> > between nab and sander).
> >
> > I'll check into this. I believe DELTAs make this effect basically go
> > away,
> > though.
> >
> > Thanks!
> > Jason
> >
> > 2011/9/30 Marek Maly <marek.maly.ujep.cz>
> >
> >> Thanks for explanation ! However after my short experiments with
> >> MMPBSA_PY
> >> I have
> >> another two interesting problems here. I did GB/PB MMPBSA_PY analysis of
> >> cationic molecule (PPI dendrimer G4, with total charge 32) to see the
> >> effect of
> >> salt parameters in GB/PB calculations. And I got these results.
> >>
> >> #1
> >> GB seems to be much much more sensitive on salt concentration (saltcon)
> >> that PB (istrng).
> >>
> >> #2
> >> Change in setting of param. "use_sander" (0/1) has practically zero
> >> influence on GB result but
> >> in case of PB there are some non-negligible differences, although these
> >> might vanish in case
> >> of calculation dH if the same shift is for complex, and
> >> (receptor+ligand).
> >>
> >> #1 and #2 are nicely illustrated by table below (H analysis of above
> >> mentioned molecule).
> >>
> >>
> >> Is there any explanation for #1 and/or #2 ?
> >>
> >> Thanks a lot in advance !
> >>
> >> Best wishes,
> >>
> >> Marek
> >>
> >>
> >> use_sander=0
> >>
> >> GB saltcon=0.0
> >> TOTAL -307.6173 20.0845
> >> 2.0085
> >> GB saltcon=0.1
> >> TOTAL -395.5508 20.0667
> >> 2.0067
> >>
> >> PB istrng=0.0
> >> TOTAL -447.0705 18.9268
> >> 1.8927
> >> PB istrng=0.1
> >> TOTAL -447.5793 18.9518
> >> 1.8952
> >>
> >>
> >> use_sander=1
> >>
> >> GB saltcon=0.0
> >> TOTAL -307.6805 20.0847
> >> 2.0085
> >> GB saltcon=0.1
> >> TOTAL -395.6140 20.0669
> >> 2.0067
> >>
> >> PB istrng=0.0
> >> TOTAL -454.1829 18.8272
> >> 1.8827
> >> PB istrng=0.1
> >> TOTAL -454.7201 18.8393
> >> 1.8839
> >>
> >>
> >>
> >>
> >> Dne Fri, 30 Sep 2011 21:27:36 +0200 Jason Swails
> >> <jason.swails.gmail.com>
> >> napsal/-a:
> >>
> >> > 2011/9/30 Marek Maly <marek.maly.ujep.cz>
> >> >
> >> >> Hi Jason,
> >> >>
> >> >> Thanks a lot ! The problem is solved and MMPBSA.MPI works perfectly !
> >> >>
> >> >> I would like to ask you about "saltcon" GB parameter. I am doing
> >> >> simulations under
> >> >> 0.15 M of NaCl. Is it in your opinion this concentration still
> >> >> acceptable
> >> >> for GB,
> >> >> or is better to go on 0.1 to be still in safe range regarding
> >> >> assumptions/approximations
> >> >> in GB theory ?
> >> >>
> >> >
> >> > 0.15 seems safe, I'm not sure. GB is fast enough that you could try
> >> > different values and see if it really makes a difference.
> >> >
> >> >
> >> >>
> >> >>
> >> >> I am also curious why usage of sander ( use_sander=1 ) causes so
> >> >> significant slowdown comparing
> >> >> to case when mmpbsa_py_energy is used ( use_sander=0 ) .
> >> >>
> >> >
> >> > I think this is because sander calculates the energy twice for some
> >> > reason
> >> > (an "initial" call and then one on the first step, perhaps). In any
> >> > case,
> >> > we've found that using the nab program gives ~2x speedup for both GB
> >> and
> >> > PB. I haven't done my own code investigation to find out where this
> >> is
> >> > being done, I just took it on faith based on what someone (I've
> >> forgotten
> >> > who at this point) told me. We suggest *not* setting use_sander=1
> >> unless
> >> > you absolutely have to (for instance, if you're using chamber
> >> prmtops, or
> >> > some of the GB models not implemented in nab, or QM/MM-GBSA).
> >> >
> >> > HTH,
> >> > Jason
> >> >
> >> >
> >> >> Thanks once again !
> >> >>
> >> >> Best wishes,
> >> >>
> >> >> Marek
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >> Dne Fri, 30 Sep 2011 07:10:47 +0200 Jason Swails
> >> >> <jason.swails.gmail.com>
> >> >> napsal/-a:
> >> >>
> >> >> > Hi,
> >> >> >
> >> >> > MMPBSA.py.MPI is built when you build AmberTools 1.5 in parallel,
> >> not
> >> >> > Amber
> >> >> > 11. Thus, running "make parallel" in $AMBERHOME/AmberTools/src
> >> after
> >> >> > running ./configure -mpi gnu is what you need to do. (You could
> >> also
> >> >> go
> >> >> > to
> >> >> > the $AMBERHOME/AmberTools/src/mmpbsa_py directory and run the "make
> >> >> > parallel" command -- it should build it for you).
> >> >> >
> >> >> > About the errors you're seeing -- this is a sign that your
> >> environment
> >> >> > variables or something may be out of whack. I suggest trying to
> >> >> > recompile
> >> >> > AmberTools 1.5 in serial, then in parallel.
> >> >> >
> >> >> > HTH,
> >> >> > Jason
> >> >> >
> >> >> > 2011/9/29 Marek Maly <marek.maly.ujep.cz>
> >> >> >
> >> >> >> Hi Jason,
> >> >> >> thanks for a prompt reply !
> >> >> >>
> >> >> >> Regarding #1 I tried your suggestion and it works perfectly !
> >> >> >>
> >> >> >> Regarding #2 I didn't find MMPBSA.MPI in $AMBERHOME/bin nor
> >> >> >>
> >> >> >> MMPBSA.py.MPI which I suppose to be located in
> >> >> >> $AMBERHOME/AmberTools/src/mmpbsa_py
> >> >> >> where I found MMPBSA.py script. Then I found in Amber11 manual :
> >> >> >>
> >> >> >>
> >> >> >>
> >> >>
> >>
> -------------------------------------------------------------------------------------
> >> >> >> 10.3.3.2 Parallel (MPI) version
> >> >> >> This version is installed with Amber during the parallel install.
> >> The
> >> >> >> python package mpi4py is included with the MMPBSA.py source code
> >> and
> >> >> >> must
> >> >> >> be successfully installed in order to run the MPI version of
> >> MMPBSA
> >> >> >> ......
> >> >> >>
> >> >> >>
> >> >> >>
> >> >>
> >>
> --------------------------------------------------------------------------------------
> >> >> >>
> >> >> >> So I successfully installed also parallel version (./configure
> >> -mpi
> >> >> gnu)
> >> >> >> of Amber11 ( having before just serial one in combination with
> >> >> >> AmberTools1.5 just for analyses of MD trajectories calculated
> >> with
> >> >> >> pmemd.CUDA on separate CUDA WorkStations. ), but unfortunately
> >> >> situation
> >> >> >> didn.t change i.e. no MMPBSA.MPI appeared in $AMBERHOME/bin. So I
> >> >> went
> >> >> >> to
> >> >> >> $AMBERHOME/AmberTools/src/mmpbsa_py and tried "make install"
> >> >> >> after this I have obtained plethora of errors please see below. I
> >> >> would
> >> >> >> be
> >> >> >> really grateful for any helpful suggestion ! Anyway that "forking"
> >> >> >> parallel approach from mm_pbsa.pl might be fully sufficient and
> >> >> useful
> >> >> >> alternative for those who don.t care about parallel Amber11
> >> >> >> installation or even don.t care about MPI on their machine or they
> >> >> have
> >> >> >> simply problem to install these things.
> >> >> >> For those might be parallelization of MMPBSA jobs although
> >> limited
> >> >> to
> >> >> >> given node sufficient solution.
> >> >> >> But there are for sure much more important development tasks in
> >> the
> >> >> >> queue
> >> >> >> I guess :))
> >> >> >>
> >> >> >> Thanks in advance for your help !
> >> >> >>
> >> >> >>
> >> >> >> Best wishes,
> >> >> >>
> >> >> >> Marek
> >> >> >>
> >> >> >>
> >> >> >> mmaly.node25
> >> ~/_applications/amber11_node25/AmberTools/src/mmpbsa_py
> >> >> $
> >> >> >> make install
> >> >> >> make: Warning: File `../config.h' has modification time 8.3e+03 s
> >> in
> >> >> the
> >> >> >> future
> >> >> >> /bin/bash setup.sh
> >> >> >> Using AmberTools' python
> >> >> >> /home/mmaly/_applications/amber11_node25/bin/nab -o
> >> >> mmpbsa_py_nabnmode
> >> >> >> mmpbsa_entropy.nab
> >> >> >> /home/mmaly/_applications/amber11/lib/arpack.a(dsaupd.o): In
> >> function
> >> >> >> `dsaupd_':
> >> >> >> dsaupd.f:(.text+0x11d): undefined reference to
> >> >> >> `_gfortran_compare_string'
> >> >> >> dsaupd.f:(.text+0x5f9): undefined reference to
> >> `_gfortran_st_write'
> >> >> >> dsaupd.f:(.text+0x601): undefined reference to
> >> >> `_gfortran_st_write_done'
> >> >> >> dsaupd.f:(.text+0x64d): undefined reference to
> >> `_gfortran_st_write'
> >> >> >> dsaupd.f:(.text+0x65f): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> dsaupd.f:(.text+0x671): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> dsaupd.f:(.text+0x683): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> dsaupd.f:(.text+0x695): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> dsaupd.f:(.text+0x6a7): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >>
> >> >> >>
> >> >>
> >>
> /home/mmaly/_applications/amber11/lib/arpack.a(dsaupd.o):dsaupd.f:(.text+0x6b9):
> >> >> >> more undefined references to `_gfortran_transfer_integer' follow
> >> >> >> /home/mmaly/_applications/amber11/lib/arpack.a(dsaupd.o): In
> >> function
> >> >> >> `dsaupd_':
> >> >> >> dsaupd.f:(.text+0x6cb): undefined reference to
> >> >> `_gfortran_transfer_real'
> >> >> >> dsaupd.f:(.text+0x6dd): undefined reference to
> >> >> `_gfortran_transfer_real'
> >> >> >> dsaupd.f:(.text+0x6ef): undefined reference to
> >> >> `_gfortran_transfer_real'
> >> >> >> dsaupd.f:(.text+0x701): undefined reference to
> >> >> `_gfortran_transfer_real'
> >> >> >> dsaupd.f:(.text+0x713): undefined reference to
> >> >> `_gfortran_transfer_real'
> >> >> >>
> >> >> >>
> >> >>
> >>
> /home/mmaly/_applications/amber11/lib/arpack.a(dsaupd.o):dsaupd.f:(.text+0x725):
> >> >> >> more undefined references to `_gfortran_transfer_real' follow
> >> >> >> /home/mmaly/_applications/amber11/lib/arpack.a(dsaupd.o): In
> >> function
> >> >> >> `dsaupd_':
> >> >> >> dsaupd.f:(.text+0x787): undefined reference to
> >> >> `_gfortran_st_write_done'
> >> >> >> dsaupd.f:(.text+0x7a3): undefined reference to
> >> >> >> `_gfortran_compare_string'
> >> >> >> dsaupd.f:(.text+0x7c2): undefined reference to
> >> >> >> `_gfortran_compare_string'
> >> >> >> dsaupd.f:(.text+0x7e1): undefined reference to
> >> >> >> `_gfortran_compare_string'
> >> >> >> dsaupd.f:(.text+0x800): undefined reference to
> >> >> >> `_gfortran_compare_string'
> >> >> >> dsaupd.f:(.text+0x857): undefined reference to
> >> >> >> `_gfortran_compare_string'
> >> >> >>
> >> >> >>
> >> >>
> >>
> /home/mmaly/_applications/amber11/lib/arpack.a(dseupd.o):dseupd.f:(.text+0x110):
> >> >> >> more undefined references to `_gfortran_compare_string' follow
> >> >> >> /home/mmaly/_applications/amber11/lib/arpack.a(dseupd.o): In
> >> function
> >> >> >> `dseupd_':
> >> >> >> dseupd.f:(.text+0xb6d): undefined reference to
> >> >> `_gfortran_copy_string'
> >> >> >> dseupd.f:(.text+0xb8e): undefined reference to
> >> >> `_gfortran_copy_string'
> >> >> >> dseupd.f:(.text+0xc38): undefined reference to
> >> >> `_gfortran_copy_string'
> >> >> >> dseupd.f:(.text+0xc59): undefined reference to
> >> >> `_gfortran_copy_string'
> >> >> >> dseupd.f:(.text+0xcc2): undefined reference to
> >> >> >> `_gfortran_compare_string'
> >> >> >> dseupd.f:(.text+0xd60): undefined reference to
> >> >> >> `_gfortran_compare_string'
> >> >> >> dseupd.f:(.text+0xe23): undefined reference to
> >> >> >> `_gfortran_compare_string'
> >> >> >> dseupd.f:(.text+0xf6d): undefined reference to
> >> >> >> `_gfortran_compare_string'
> >> >> >> dseupd.f:(.text+0xf91): undefined reference to
> >> >> >> `_gfortran_compare_string'
> >> >> >>
> >> >> >>
> >> >>
> >>
> /home/mmaly/_applications/amber11/lib/arpack.a(dseupd.o):dseupd.f:(.text+0xfb5):
> >> >> >> more undefined references to `_gfortran_compare_string' follow
> >> >> >> /home/mmaly/_applications/amber11/lib/arpack.a(ivout.o): In
> >> function
> >> >> >> `ivout_':
> >> >> >> ivout.f:(.text+0xb7): undefined reference to `_gfortran_st_write'
> >> >> >> ivout.f:(.text+0xc6): undefined reference to
> >> >> >> `_gfortran_transfer_character'
> >> >> >> ivout.f:(.text+0xd3): undefined reference to
> >> >> >> `_gfortran_transfer_character'
> >> >> >> ivout.f:(.text+0xdb): undefined reference to
> >> >> `_gfortran_st_write_done'
> >> >> >> ivout.f:(.text+0x134): undefined reference to
> >> >> `_gfortran_st_write_done'
> >> >> >> ivout.f:(.text+0x19b): undefined reference to `_gfortran_st_write'
> >> >> >> ivout.f:(.text+0x1b0): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> ivout.f:(.text+0x1c5): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> ivout.f:(.text+0x1f7): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> ivout.f:(.text+0x239): undefined reference to `_gfortran_st_write'
> >> >> >> ivout.f:(.text+0x241): undefined reference to
> >> >> `_gfortran_st_write_done'
> >> >> >> ivout.f:(.text+0x2aa): undefined reference to
> >> >> `_gfortran_st_write_done'
> >> >> >> ivout.f:(.text+0x311): undefined reference to `_gfortran_st_write'
> >> >> >> ivout.f:(.text+0x326): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> ivout.f:(.text+0x33b): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> ivout.f:(.text+0x373): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> ivout.f:(.text+0x3ca): undefined reference to
> >> >> `_gfortran_st_write_done'
> >> >> >> ivout.f:(.text+0x431): undefined reference to `_gfortran_st_write'
> >> >> >> ivout.f:(.text+0x446): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> ivout.f:(.text+0x45b): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> ivout.f:(.text+0x48d): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> ivout.f:(.text+0x4d8): undefined reference to
> >> >> `_gfortran_st_write_done'
> >> >> >> ivout.f:(.text+0x53f): undefined reference to `_gfortran_st_write'
> >> >> >> ivout.f:(.text+0x554): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> ivout.f:(.text+0x569): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> ivout.f:(.text+0x59b): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> ivout.f:(.text+0x5da): undefined reference to
> >> >> `_gfortran_st_write_done'
> >> >> >> ivout.f:(.text+0x641): undefined reference to `_gfortran_st_write'
> >> >> >> ivout.f:(.text+0x656): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> ivout.f:(.text+0x66b): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> ivout.f:(.text+0x69d): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> ivout.f:(.text+0x6e4): undefined reference to
> >> >> `_gfortran_st_write_done'
> >> >> >> ivout.f:(.text+0x74b): undefined reference to `_gfortran_st_write'
> >> >> >> ivout.f:(.text+0x760): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> ivout.f:(.text+0x775): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> ivout.f:(.text+0x7a7): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> ivout.f:(.text+0x7ee): undefined reference to
> >> >> `_gfortran_st_write_done'
> >> >> >> ivout.f:(.text+0x855): undefined reference to `_gfortran_st_write'
> >> >> >> ivout.f:(.text+0x86a): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> ivout.f:(.text+0x87f): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> ivout.f:(.text+0x8b1): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> ivout.f:(.text+0x8ed): undefined reference to
> >> >> `_gfortran_st_write_done'
> >> >> >> ivout.f:(.text+0x954): undefined reference to `_gfortran_st_write'
> >> >> >> ivout.f:(.text+0x969): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> ivout.f:(.text+0x97e): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> ivout.f:(.text+0x9b0): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> /home/mmaly/_applications/amber11/lib/arpack.a(dvout.o): In
> >> function
> >> >> >> `dvout_':
> >> >> >> dvout.f:(.text+0xb7): undefined reference to `_gfortran_st_write'
> >> >> >> dvout.f:(.text+0xc6): undefined reference to
> >> >> >> `_gfortran_transfer_character'
> >> >> >> dvout.f:(.text+0xd3): undefined reference to
> >> >> >> `_gfortran_transfer_character'
> >> >> >> dvout.f:(.text+0xdb): undefined reference to
> >> >> `_gfortran_st_write_done'
> >> >> >> dvout.f:(.text+0x134): undefined reference to
> >> >> `_gfortran_st_write_done'
> >> >> >> dvout.f:(.text+0x19b): undefined reference to `_gfortran_st_write'
> >> >> >> dvout.f:(.text+0x1b0): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> dvout.f:(.text+0x1c5): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> dvout.f:(.text+0x1f7): undefined reference to
> >> >> `_gfortran_transfer_real'
> >> >> >> dvout.f:(.text+0x239): undefined reference to `_gfortran_st_write'
> >> >> >> dvout.f:(.text+0x241): undefined reference to
> >> >> `_gfortran_st_write_done'
> >> >> >> dvout.f:(.text+0x298): undefined reference to
> >> >> `_gfortran_st_write_done'
> >> >> >> dvout.f:(.text+0x2ff): undefined reference to `_gfortran_st_write'
> >> >> >> dvout.f:(.text+0x314): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> dvout.f:(.text+0x329): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> dvout.f:(.text+0x35b): undefined reference to
> >> >> `_gfortran_transfer_real'
> >> >> >> dvout.f:(.text+0x3a1): undefined reference to
> >> >> `_gfortran_st_write_done'
> >> >> >> dvout.f:(.text+0x408): undefined reference to `_gfortran_st_write'
> >> >> >> dvout.f:(.text+0x41d): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> dvout.f:(.text+0x432): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> dvout.f:(.text+0x464): undefined reference to
> >> >> `_gfortran_transfer_real'
> >> >> >> dvout.f:(.text+0x4a9): undefined reference to
> >> >> `_gfortran_st_write_done'
> >> >> >> dvout.f:(.text+0x510): undefined reference to `_gfortran_st_write'
> >> >> >> dvout.f:(.text+0x525): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> dvout.f:(.text+0x53a): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> dvout.f:(.text+0x56c): undefined reference to
> >> >> `_gfortran_transfer_real'
> >> >> >> dvout.f:(.text+0x5aa): undefined reference to
> >> >> `_gfortran_st_write_done'
> >> >> >> dvout.f:(.text+0x611): undefined reference to `_gfortran_st_write'
> >> >> >> dvout.f:(.text+0x626): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> dvout.f:(.text+0x63b): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> dvout.f:(.text+0x66d): undefined reference to
> >> >> `_gfortran_transfer_real'
> >> >> >> dvout.f:(.text+0x6aa): undefined reference to
> >> >> `_gfortran_st_write_done'
> >> >> >> dvout.f:(.text+0x711): undefined reference to `_gfortran_st_write'
> >> >> >> dvout.f:(.text+0x726): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> dvout.f:(.text+0x73b): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> dvout.f:(.text+0x76d): undefined reference to
> >> >> `_gfortran_transfer_real'
> >> >> >> dvout.f:(.text+0x7b5): undefined reference to
> >> >> `_gfortran_st_write_done'
> >> >> >> dvout.f:(.text+0x81c): undefined reference to `_gfortran_st_write'
> >> >> >> dvout.f:(.text+0x831): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> dvout.f:(.text+0x846): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> dvout.f:(.text+0x878): undefined reference to
> >> >> `_gfortran_transfer_real'
> >> >> >> dvout.f:(.text+0x8a6): undefined reference to
> >> >> `_gfortran_st_write_done'
> >> >> >> dvout.f:(.text+0x90c): undefined reference to `_gfortran_st_write'
> >> >> >> dvout.f:(.text+0x921): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> dvout.f:(.text+0x936): undefined reference to
> >> >> >> `_gfortran_transfer_integer'
> >> >> >> dvout.f:(.text+0x968): undefined reference to
> >> >> `_gfortran_transfer_real'
> >> >> >> /home/mmaly/_applications/amber11/lib/arpack.a(dsaup2.o): In
> >> function
> >> >> >> `dsaup2_':
> >> >> >> dsaup2.f:(.text+0xb4d): undefined reference to
> >> >> >> `_gfortran_compare_string'
> >> >> >> dsaup2.f:(.text+0xb71): undefined reference to
> >> >> `_gfortran_copy_string'
> >> >> >> dsaup2.f:(.text+0xcde): undefined reference to
> >> >> `_gfortran_copy_string'
> >> >> >> dsaup2.f:(.text+0xd77): undefined reference to
> >> >> >> `_gfortran_compare_string'
> >> >> >> dsaup2.f:(.text+0xd9b): undefined reference to
> >> >> `_gfortran_copy_string'
> >> >> >> dsaup2.f:(.text+0xef8): undefined reference to
> >> >> >> `_gfortran_compare_string'
> >> >> >> dsaup2.f:(.text+0xf19): undefined reference to
> >> >> >> `_gfortran_compare_string'
> >> >> >> dsaup2.f:(.text+0xf3a): undefined reference to
> >> >> >> `_gfortran_compare_string'
> >> >> >> dsaup2.f:(.text+0xf5b): undefined reference to
> >> >> >> `_gfortran_compare_string'
> >> >> >> dsaup2.f:(.text+0x104a): undefined reference to
> >> >> `_gfortran_copy_string'
> >> >> >> dsaup2.f:(.text+0x106b): undefined reference to
> >> >> `_gfortran_copy_string'
> >> >> >> dsaup2.f:(.text+0x108c): undefined reference to
> >> >> `_gfortran_copy_string'
> >> >> >> dsaup2.f:(.text+0x10ad): undefined reference to
> >> >> `_gfortran_copy_string'
> >> >> >> /home/mmaly/_applications/amber11/lib/arpack.a(dsesrt.o): In
> >> function
> >> >> >> `dsesrt_':
> >> >> >> dsesrt.f:(.text+0x55): undefined reference to
> >> >> `_gfortran_compare_string'
> >> >> >> dsesrt.f:(.text+0x18c): undefined reference to
> >> >> >> `_gfortran_compare_string'
> >> >> >> dsesrt.f:(.text+0x2e0): undefined reference to
> >> >> >> `_gfortran_compare_string'
> >> >> >> dsesrt.f:(.text+0x3fe): undefined reference to
> >> >> >> `_gfortran_compare_string'
> >> >> >> /home/mmaly/_applications/amber11/lib/arpack.a(dsgets.o): In
> >> function
> >> >> >> `dsgets_':
> >> >> >> dsgets.f:(.text+0x5d): undefined reference to
> >> >> `_gfortran_compare_string'
> >> >> >> cc failed!
> >> >> >> make: *** [install] Error 1
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> Dne Fri, 30 Sep 2011 00:12:20 +0200 Jason Swails
> >> >> >> <jason.swails.gmail.com>
> >> >> >> napsal/-a:
> >> >> >>
> >> >> >> > Hello,
> >> >> >> >
> >> >> >> > On Thu, Sep 29, 2011 at 5:32 PM, Marek Maly <marek.maly.ujep.cz
> >
> >> >> >> wrote:
> >> >> >> >
> >> >> >> >> Dear all,
> >> >> >> >> I just started today with MMPBSA.py (until now I used
> >> mm_pbsa.pl
> >> ).
> >> >> >> >>
> >> >> >> >> After the relevant tutorial and brief reading of MMPBSA.py
> >> manual
> >> >> I
> >> >> >> have
> >> >> >> >> these two questions.
> >> >> >> >>
> >> >> >> >> #1
> >> >> >> >>
> >> >> >> >> How to proceed with MMPBSA.py if I want to calculate just
> >> >> (absolute)
> >> >> >> >> free
> >> >> >> >> energy of the given molecule
> >> >> >> >> (not dG of binding between receptor and ligand molecules).
> >> >> >> >>
> >> >> >> >
> >> >> >> > Just supply a complex prmtop file. If you don't provide a
> >> >> receptor or
> >> >> >> > ligand topology file, you will get this same behavior.
> >> >> >> >
> >> >> >> >
> >> >> >> >>
> >> >> >> >>
> >> >> >> >> In case of mm_pbsa.pl one could set just COMPLEX, RECEPTOR,
> >> LIGAND
> >> >> >> flags
> >> >> >> >> in input file like this:
> >> >> >> >>
> >> >> >> >>
> >> >> >> >>
> >> >> >> >> COMPLEX 0
> >> >> >> >> RECEPTOR 1
> >> >> >> >> LIGAND 0
> >> >> >> >>
> >> >> >> >>
> >> >> >> >> and mm_pbsa.pl will consider here the stand-alone molecule
> >> >> provided
> >> >> >> as
> >> >> >> >> the "formal receptor" without any complains
> >> >> >> >> that complex or ligand are not specified and calculate just H
> >> or
> >> >> S of
> >> >> >> >> that
> >> >> >> >> molecule. Is there any way how to
> >> >> >> >> tell MMPBSA.py that I want just calculate H, S or whole G for
> >> the
> >> >> >> given
> >> >> >> >> molecule ?
> >> >> >> >>
> >> >> >> >>
> >> >> >> >>
> >> >> >> >> #2
> >> >> >> >>
> >> >> >> >> In mm_pbsa.pl there is available flag PARALLEL which is very
> >> >> useful
> >> >> >> as
> >> >> >> >> it
> >> >> >> >> allows to define howmany frames
> >> >> >> >> from the given trajectory will be processed simultaneously. So
> >> >> for
> >> >> >> >> example
> >> >> >> >> if one has node
> >> >> >> >> with 8 CPU cores, setting:
> >> >> >> >>
> >> >> >> >> PARALLEL 8
> >> >> >> >>
> >> >> >> >> allow to process 8 MD frames simultaneously (probably without
> >> >> need of
> >> >> >> >> MPI
> >> >> >> >> ?).
> >> >> >> >>
> >> >> >> >
> >> >> >> > Yes. The way mm_pbsa.pl works is by forking off processes.
> >> This
> >> >> >> limits
> >> >> >> > parallel performance to a single node, though, since the simple
> >> >> forker
> >> >> >> > doesn't know enough to launch processes on remote nodes. MPI,
> >> on
> >> >> the
> >> >> >> > other
> >> >> >> > hand, is built for normal, parallel Amber simulations and is
> >> easily
> >> >> >> run
> >> >> >> > on
> >> >> >> > distributed systems (across multiple nodes). Since there were
> >> good
> >> >> >> > python
> >> >> >> > bindings for MPI, we decided to use MPI to parallelize
> >> MMPBSA.py.
> >> >> >> >
> >> >> >> >
> >> >> >> >> In case of python version just usage of MMPBSA.py.MPI instead
> >> >> >> MMPBSA.py
> >> >> >> >> brings the similar
> >> >> >> >> possibility am I right ?
> >> >> >> >>
> >> >> >> >
> >> >> >> > Correct. mpi4py is built automatically with AmberTools 1.5. I
> >> >> would
> >> >> >> > suggest using AmberTools 1.5 version, in which case you have to
> >> use
> >> >> >> > MMPBSA
> >> >> >> > and MMPBSA.MPI, which are shell scripts that invoke MMPBSA.py
> >> and
> >> >> >> > MMPBSA.py.MPI with the appropriate variables.
> >> >> >> >
> >> >> >> > HTH,
> >> >> >> > Jason
> >> >> >> >
> >> >> >>
> >> >> >>
> >> >> >> --
> >> >> >> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
> >> >> >> http://www.opera.com/mail/
> >> >> >>
> >> >> >> _______________________________________________
> >> >> >> AMBER mailing list
> >> >> >> AMBER.ambermd.org
> >> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >>
> >> >> >
> >> >> >
> >> >> >
> >> >>
> >> >>
> >> >> --
> >> >> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
> >> >> http://www.opera.com/mail/
> >> >>
> >> >> _______________________________________________
> >> >> AMBER mailing list
> >> >> AMBER.ambermd.org
> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >>
> >> >
> >> >
> >> >
> >>
> >>
> >> --
> >> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
> >> http://www.opera.com/mail/
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
>
>
> --
> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
> http://www.opera.com/mail/
>
> _______________________________________________
> 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
Received on Fri Sep 30 2011 - 16:00:02 PDT
