Yes I know about the sander.APBS possibility but I have not installed it
yet.
Regarding GB/Amber PB salt sensitivity, it is clear that this should be
system dependent as it is in reality. I know, bulk concentration 0.1 M of
NaCl
is not so much and will probably not influence much absolute free energy
(free energy of binding) in case of neutral
molecules but has indeed significantly stronger impact in case of charged
molecules because then
relevant counter ions are going from the bulk solvent to the very close
proximity of that
charged molecule/s and screen their surface charges or in other words
change locally
dielectric constant of solvent and indeed in case of such charged solutes
this salt effect should
significantly decrease the enthalpy (make it "more negative" or in anothe
words increase the absolute value) as the positive
contribution arising from interactions of the same charges on charged
molecule is decreased
(by screening effect). I really don't know how much realistically are
these effects implemented in GB/PB
methods but to me the actual response of Amber implementation of GB model
seems to be more
realistic that response of Amber implementation of linear PB (practically
zero response).
To be frank I didn't care much about saltcon/istrng parameters in the past
having
there their default values ( 0 in mm_pbsa.pl). So in fact I assumed here
just structural
effects (on simulated standalone molecules, complexes) which was created
during MD run due to
interaction of ions with the solute/s. But recently I simulated and
analysed several
complexes (DNA + several dendrimers (differently positively
charged/uncharged)). I
wanted to compare stability of final clusters obtained in 40ns runs by
estimate
the energy necessary to destroy the final molecular cluster (
G(cluster)-SUM{Gi} where i is going
over all molecules from which final cluster is composed ).
In case of unmodified PPI dendrimers (so fully charged +32) I have
obtained flexible cluster where
several of these molecules was attached to the DNA in chain manner like
this:
O;
;O
O;
;
O;
;
;
;O
;
O;
where ";" stands for parts of DNA and "O" are dendrimers.
So flexible but pretty stable complex. After GB/PB analysis with usual
saltcon/istrng=0 setting I have obtained
huge positive numbers for the total cluster binding energy around
1000kcal/mol suggesting that this cluster
should never be created. So probably for pure water this prediction is
right and Dendrimer/DNA (+/-) interactions
might not overcome DEN/DEN (+/+) interactions/repulsions. But that stable
complex was obtained from MD
simulation with 0.15 M NaCl in the box. So I got the idea to adjust
properly this time also saltcon/istrng
parameters which didn't changed PB result but from GB I have obtained nice
dH = -349kcal/mol and together
with dS I have obtained dG=-78 kcal/mol in very good context with the
other clusters.
So it seems to me that in case of charged molecules the proper setting of
saltcon/istrng parameters is important
and thanks to above experience I started to believe a bit more to GB
however in theory PB should be more realistic model.
OK maybe GB overestimate the salt effect but again speaking about DELTAS
it may provide more realistic results.
On the other hand Amber implementation of linear PB has really almost zero
sensitivity to relevant salt parameter (istrng) within
the given range (around 0.1) which does not reflect the reality in some
specific cases (strongly charged solutes).
If I have time I would really compare salt sensitivity of Amber native PB
solver with that APBS ...
I also found very interesting notice in AmberTools.pdb
---------------AmberTools.pdf--page-158------------------------------------------------------------------------------
The salt term in the PB equation can be linearized when the Boltzmann
factor is close to zero.
However, the approximation apparently does not hold in highly charged
systems.
Thus, it is recommended that the full nonlinear PB equation solvers be
used in such systems.
------------------------------------------------------------------------------------------------
So first of all I will start to experiment with nonlinear Amber PB solver
to see the effect.
Anyway if you have meanwhile any relevant response from your PB/GB
colleagues, I would be grateful for them as well.
Below is my table where I added also the case of 1M concentration.
Best wishes,
Marek
use_sander=0
#GB
saltcon=0.0 TOTAL -307.6173
saltcon=0.1 TOTAL -395.5508
saltcon=1.0 TOTAL -433.9759
#linear PB
istrng=0.0 TOTAL -447.0705
istrng=0.1 TOTAL -447.5793
istrng=1.0 TOTAL -448.6026
Dne Sat, 01 Oct 2011 00:55:26 +0200 Jason Swails <jason.swails.gmail.com>
napsal/-a:
> 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
>>
>
>
>
--
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
Received on Fri Sep 30 2011 - 21:00:02 PDT
