HI Jason,
Thanks a lot, now it works, but it gives me the following error:
Error opening unit 30: File "_MMPBSA_dummycomplex.inpcrd" is missing or unreadable
Error opening unit 30: File "_MMPBSA_dummycomplex.inpcrd" is missing or unreadable
Error opening unit 30: File "_MMPBSA_dummycomplex.inpcrd" is missing or unreadable
CalcError: /usr/local/amber12/bin/sander failed with prmtop com_t9.top!
Error occured on rank 3.
Here is my input:
&general
startframe=1, endframe=8, verbose=1, search_path=1
/
&gb
igb=5, ifqnt=1, qm_residues="291, 22-27", qm_theory="PM3"
/
The same job with the same settings runs perfectly when i remove the [, ifqnt=1, qm_residues="291, 22-27", qm_theory="PM3"] section.
Regards
Marawan
________________________________
From: Jason Swails <jason.swails.gmail.com>
To: marawan hussain <marawanhussain.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Friday, 4 January 2013 11:47 AM
Subject: Re: [AMBER] MMPBSA error
Ah. I did not realize you were installing serial and parallel programs to
different places. Since MMPBSA.py.MPI calls serial programs on each
thread, you need the serial executables to be able to use MMPBSA.py.MPI.
If you add the serial Amber installation to your PATH, you can add the
variable "search_path=1" to your &general section to force MMPBSA.py to
search the PATH if mmpbsa_py_energy is not in $AMBERHOME/bin.
HTH,
Jason
P.S. The alternative is, of course, to install the serial and parallel
versions to the same place.
On Thu, Jan 3, 2013 at 6:10 PM, marawan hussain <marawanhussain.yahoo.com>wrote:
> Hi Jason,
> I got this message from the installtion team, could you please suggest if
> something is going wrong:
>
>
> Here is a snippet from AmberTools/src/Makefile:
>
> parallel: configured_parallel THIRDPARTY
>
> (cd mmpbsa_py && $(MAKE) parallel )
>
> So, when building the parallel Amber the contents of mmpbsa_py are built
> with the "parallel" target. Let's see what that does, here is a snippet
> from AmberTools/src/mmpbsa_py/Makefile:
>
> install:
> /bin/bash setup.sh $(BINDIR) $(PYTHON)
> $(BINDIR)/nab -o mmpbsa_py_nabnmode mmpbsa_entropy.nab
> /bin/mv mmpbsa_py_nabnmode $(BINDIR)
> $(BINDIR)/nab -o mmpbsa_py_energy mmpbsa_energy.nab
> /bin/mv mmpbsa_py_energy $(BINDIR)
>
> serial: install
>
> parallel:
> /bin/bash setup.sh $(BINDIR) $(PYTHON) par
>
> You can see that only in the serial version does it copy across
> "mmpbsa_py_energy".
>
>
>
> Regards
> Marawan
>
>
> ________________________________
> From: Jason Swails <jason.swails.gmail.com>
> To: marawan hussain <marawanhussain.yahoo.com>; AMBER Mailing List <
> amber.ambermd.org>
> Sent: Thursday, 3 January 2013 11:43 PM
> Subject: Re: [AMBER] MMPBSA error
>
> MMPBSA.py looks for the various programs inside $AMBERHOME/bin, not in the
> $PATH (by default, at least). It would seem as though $AMBERHOME is not
> set correctly for your parallel calculations.
>
> HTH,
> Jason
>
> On Thu, Jan 3, 2013 at 12:11 AM, marawan hussain
> <marawanhussain.yahoo.com>wrote:
>
> > Dear AMBER developers,
> > I'm trying to run an MMPBSA.py.MPI job but i got the following error:
> >
> > MMPBSA_Error: Could not find necessary program [mmpbsa_py_energy]
> > Error occured on rank 0.
> > Exiting. All files have been retained.
> >
> > I tried to to set the path of the (mmpbsa_py_energy) program explicitly
> in
> > the script but this didn't solve the problem.
> >
> > export PATH=/lustre/projects/p012_swin/mahmed/HER2/pbsa_test:$PATH
> >
> >
> >
> > I'm noticing that the serial version has the program in ($AmberTools/bin)
> > but the parallel version does't have it
> > We tried to re-install MMPBSA by "make install" or "make parallel" but
> > this didn't solve the problem.
> > Any suggestion will be appreciated
> >
> > Regards
> > Marawan
> > _______________________________________________
> > 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
> _______________________________________________
> 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
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Received on Thu Jan 03 2013 - 18:30:04 PST
