Hi All,
After getting suggestions from you I have upgraded my AmberTools from
AmberTools 1.5 to AmberTools12. But even after doing that I'm getting
another error message different from the earlier. I have copied both the
error messages. it would be great if you would have suggestions regarding
further proceedings.
*Error message ** After Upgradation : (When I have Amber 11 with
AmberTools 12)*
saugata.saugata:~$ cd Desktop/ba2291/mdrun/ba2291_atp
saugata.saugata:~/Desktop/ba2291/mdrun/ba2291_atp$ $AMBERHOME/bin/MMPBSA -O
-i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp ba2291_atp_mg.prmtop -cp
ba2291_com.prmtop -rp ba2291_prot.prmtop -lp atp.prmtop -y *.mdcrd
bash: /home/saugata/amber12/bin/MMPBSA: No such file or directory
saugata.saugata:~/Desktop/ba2291/mdrun/ba2291_atp$ $AMBERHOME/bin/MMPBSA.py
-O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp ba2291_atp_mg.prmtop -cp
ba2291_com.prmtop -rp ba2291_prot.prmtop -lp atp.prmtop -y *.mdcrd
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /home/saugata/amber12/bin/mmpbsa_py_energy
cpptraj found! Using /home/saugata/amber12/bin/cpptraj
Preparing trajectories for simulation...
50 frames were processed by cpptraj for use in calculation.
Beginning GB calculations with /home/saugata/amber12/bin/mmpbsa_py_energy
calculating complex contribution...
calculating receptor contribution...
mmpbsa_py_energy: malloc.c:3801: _int_malloc: Assertion `(unsigned
long)(size) >= (unsigned long)(nb)' failed.
CalcError: /home/saugata/amber12/bin/mmpbsa_py_energy failed with prmtop
ba2291_prot.prmtop!
Exiting. All files have been retained.
saugata.saugata:~/Desktop/ba2291/mdrun/ba2291_atp$
*Error message Before Upgradation: (When I had Amber 11 with AmberTools 1.5)
*
saugata.saugata:~/Desktop/
ba2291/mdrun/ba2291_atp$ $AMBERHOME/bin/MMPBSA -O -i mmpbsa.in -o
FINAL_RESULTS_MMPBSA.dat -sp ba2291_atp_mg.prmtop -cp ba2291_com.prmtop -rp
ba2291_prot.prmtop -lp atp.prmtop -y *.mdcrd
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
ptraj found! Using /home/saugata/amber11/bin/ptraj
mmpbsa_py_energy found! Using /home/saugata/amber11/bin/mmpbsa_py_energy
for GB calculations
mmpbsa_py_energy found! Using /home/saugata/amber11/bin/mmpbsa_py_energy
for PB calculations
Preparing trajectories for simulation...
50 frames were read in and processed by ptraj for use in calculation.
Beginning GB calculations with mmpbsa_py_energy...
calculating complex contribution...
calculating receptor contribution...
Segmentation fault (core dumped)
Error: mmpbsa_py_energy error during GB calculations!
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
--clean to erase these files.
saugata.saugata:~/Desktop/ba2291/mdrun/ba2291_atp$ MMPBSA.py --clean
MMPBSA.py: command not found
saugata.saugata:~/Desktop/ba2291/mdrun/ba2291_atp$ MMPBSA --clean
Reading command-line arguments and input files...
Cleaning temporary files
saugata.saugata:~/Desktop/ba2291/mdrun/ba2291_atp$
Thanks,
Saugata
On Tue, Feb 19, 2013 at 9:43 AM, Jason Swails <jason.swails.gmail.com>wrote:
> On Tue, Feb 19, 2013 at 9:31 AM, Saugata Hazra <saugata.iitk.gmail.com
> >wrote:
>
> > Thank you very much Jason.
> > One more question to make it sure.
> > As I have mentioned earlier, that I have Amber 11 & AmberTools 1.5.
> > So, is it enough to upgrade only the AmberTool or I also have to upgrade
> my
> > AMBER to AMBER12.
> >
>
> Upgrading AmberTools is sufficient for MMPBSA.py.
>
>
> > Thanks,
> > Saugata
> >
> > On Tue, Feb 19, 2013 at 9:00 AM, Jason Swails <jason.swails.gmail.com
> > >wrote:
> >
> > > On Tue, Feb 19, 2013 at 8:02 AM, Saugata Hazra <saugata.iitk.gmail.com
> > > >wrote:
> > >
> > > > Hi,
> > > >
> > > > I am running a binding energy calculation (MM-PBSA) for
> protein-ligand
> > > > complex using Amber11 and AmberTools 1.5. I am following Ross Walker
> > > > tutorial but have got error message during MMPBSA calculation as
> > follows:
> > > >
> > > > saugata.saugata:~/Desktop/ba2291/mdrun/ba2291_atp$
> > $AMBERHOME/bin/MMPBSA
> > > > -O
> > > > -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp ba2291_atp_mg.prmtop
> -cp
> > > > ba2291_com.prmtop -rp ba2291_prot.prmtop -lp atp.prmtop -y *.mdcrd
> > > > Reading command-line arguments and input files...
> > > > Loading and checking parameter files for compatibility...
> > > > ptraj found! Using /home/saugata/amber11/bin/ptraj
> > > > mmpbsa_py_energy found! Using
> > /home/saugata/amber11/bin/mmpbsa_py_energy
> > > > for GB calculations
> > > > mmpbsa_py_energy found! Using
> > /home/saugata/amber11/bin/mmpbsa_py_energy
> > > > for PB calculations
> > > > Preparing trajectories for simulation...
> > > > 50 frames were read in and processed by ptraj for use in calculation.
> > > >
> > > > Beginning GB calculations with mmpbsa_py_energy...
> > > > calculating complex contribution...
> > > > calculating receptor contribution...
> > > > Segmentation fault (core dumped)
> > > >
> > >
> > > Yikes. A segfault from NAB. Try upgrading to AmberTools 12 and use
> that
> > > version instead. You can also try putting "use_sander=1" in the
> &general
> > > section of the MMPBSA.py input file to force it to use sander instead.
> > >
> > > Good luck,
> > > Jason
> > >
> > > --
> > > 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
> > >
> >
> >
> >
> > --
> >
> > *Know me Know fun, no me no fun!!!*
> > Dr. Saugata Hazra
> > _______________________________________________
> > 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
>
--
*Know me Know fun, no me no fun!!!*
Dr. Saugata Hazra
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Received on Wed Feb 20 2013 - 00:30:02 PST
