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.
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/
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Received on Fri Sep 30 2011 - 15:00:03 PDT
