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/
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Received on Thu Sep 29 2011 - 20:00:03 PDT
