Hi Bilal,
I have run the ante-MMPBSA.py script using the following on the command
line:
../../../soft/rhel6/amber/intel/mpi/14/amber14/bin/ante-MMPBSA.py -p
../../../../../../INO/sim1/PREP/GRL_INO_solvate.top -c
top/GRL_INO_nowat.top -r top/native_nowat.top -l top/LINO_nowat.top -s
3214-39717 -m 3135-3213
It does not let me specify both -m and -n for the receptor and ligand is
that correct? This script generated 3 identical topology files for me
instead of writing and complex, receptor, and ligand topology separately.
Have I typed something incorrectly? the -s is asking for the water atoms
only, correct? Thank you!
On Fri, Aug 12, 2016 at 3:15 AM, Bilal Nizami <nizamibilal1064.gmail.com>
wrote:
> Hi JoAnne,
>
> Try making the dry complex, receptor and ligand topology file from solvated
> complex topology file using anteMMPBSA.
> It helped me sometime to avoid error with topology/trajectory with
> MMPBSA.py. You can use following command:
>
> *ante-MMPBSA.py -p *GRL_INO_solvate*.top -c *GRL_INO_nowat.top* -r *
> native_nowat.top* -l *LINO_nowat.top * -s <atom mask> -m <atom mask>*
>
> You can check amber manual for details of the ante-MMPBSA.py.
>
>
> Regards,
>
> 2016-08-11 20:49 GMT+02:00 Hai Nguyen <nhai.qn.gmail.com>:
>
> > I am not familiar enough with MMGBSA code so can not provide useful debug
> > info.
> >
> > While waiting for other's feedback, you can try to upgrade to
> ambertools16:
> > http://ambermd.org/AmberTools16-get.html
> >
> > Hai
> >
> > On Thu, Aug 11, 2016 at 2:41 PM, JoAnne Babula <jbabula.umail.iu.edu>
> > wrote:
> >
> > > Hi Hai,
> > >
> > > Yes cpptraj successfully reads the mdcrd. I can also use the
> > > GRL_INO_nowat.top to view the mdcrd with VMD.
> > >
> > > On Thu, Aug 11, 2016 at 2:32 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> > >
> > > > are you able to read GRL_INO_nowat.mdcrd with cpptraj?
> > > >
> > > > Hai
> > > >
> > > > On Thu, Aug 11, 2016 at 11:21 AM, JoAnne Babula <
> jbabula.umail.iu.edu>
> > > > wrote:
> > > >
> > > > > Hello,
> > > > >
> > > > > I am trying to run a free energy calculation using 3 trajectories
> > with
> > > > > MMPBSA. I received this error with the mdcrd for the complex:
> > > > >
> > > > > Error: In GRL_INO_nowat.mdcrd, expect only 3 or 6 box coords, got 4
> > > > > Error: Box line=[ -17.791 15.073 -3.686 -19.485
> > > > > ]
> > > > > Error: Could not set up GRL_INO_nowat.mdcrd for reading.
> > > > > Error: Could not set up input trajectory 'GRL_INO_nowat.mdcrd'.
> > > > > File "/N/soft/rhel6/amber/intel/mpi/14/amber14/bin/MMPBSA.py.
> MPI",
> > > > line
> > > > > 103, in <module>
> > > > > app.file_setup()
> > > > > File "/N/soft/rhel6/amber/intel/mpi/14/amber14/lib/python2.7/
> > > > > site-packages/MMPBSA_mods/main.py", line 156, in file_setup
> > > > > self.mpi_size, str(external_progs['cpptraj']), self.pre)
> > > > > File "/N/soft/rhel6/amber/intel/mpi/14/amber14/lib/python2.7/
> > > > > site-packages/MMPBSA_mods/make_trajs.py", line 59, in
> > > make_trajectories
> > > > > traj = Trajectory(FILES.solvated_prmtop, FILES.mdcrd, cpptraj)
> > > > > File "/N/soft/rhel6/amber/intel/mpi/14/amber14/lib/python2.7/
> > > > > site-packages/MMPBSA_mods/make_trajs.py", line 467, in __init__
> > > > > self.Query()
> > > > > File "/N/soft/rhel6/amber/intel/mpi/14/amber14/lib/python2.7/
> > > > > site-packages/MMPBSA_mods/make_trajs.py", line 602, in Query
> > > > > raise TrajError('%s failed when querying %s' % (self.exe,
> traj))
> > > > > TrajError: /N/soft/rhel6/amber/intel/mpi/14/amber14/bin/cpptraj
> > failed
> > > > > when
> > > > > querying GRL_INO_nowat.mdcrd
> > > > > Error occured on rank 0.
> > > > > Exiting. All files have been retained.
> > > > >
> > > > >
> > > > >
> > > > > Do you know why this may have happened? Here is my input:
> > > > > ###Input file for running PB and GB####
> > > > > cat <<eof > mmpbsa.in
> > > > > Input file for running PB and GB
> > > > > &general
> > > > > startframe=20000, interval=80, endframe=120000, keep_files=2,
> > > > > /
> > > > > &gb
> > > > > igb=2, saltcon=0.100,
> > > > > /
> > > > > &pb
> > > > > istrng=0.100,
> > > > > /
> > > > > eof
> > > > > mpirun -n 4 MMPBSA.py.MPI -O -i mmpbsa.in -o pbsa_karst.dat -sp
> > > > > ../../../../../INO/sim1/PREP/GRL_INO_solvate.top -cp
> > > > > ../../../../../INO/sim1/PREP/GRL_INO_nowat.top -rp
> > > > > ../../../../../Native/sim_1/PREP/native_nowat.top -lp
> > > > > ../../PREP/LINO_nowat.top -y GRL_INO_nowat.mdcrd -yr
> > native_nowat.mdcrd
> > > > -yl
> > > > > LINO_nowat.mdcrd >progress
> > > > >
> > > > >
> > > > >
> > > > > Thank you so much.
> > > > >
> > > > > --
> > > > > Very Respectfully,
> > > > >
> > > > > JoAnne J Babula
> > > > > Ph.D. Candidate, IUSM, Dept. of Pharmacology
> > > > > U.S. Army, 1LT, MS
> > > > > _______________________________________________
> > > > > 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
> > > >
> > >
> > >
> > >
> > > --
> > > Very Respectfully,
> > >
> > > JoAnne J Babula
> > > Ph.D. Candidate, IUSM, Dept. of Pharmacology
> > > U.S. Army, 1LT, MS
> > > _______________________________________________
> > > 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
> >
>
>
>
> --
> *Bilal Nizami*
> School of Health Sciences
> University of KwaZulu-Natal
> Durban
> 4000
> South Africa
>
> Linkedin: za.linkedin.com/pub/bilal-nizami/49/673/790/
> Email: 214573074.stu.ukzn.ac.za
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Very Respectfully,
JoAnne J Babula
Ph.D. Candidate, IUSM, Dept. of Pharmacology
U.S. Army, 1LT, MS
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Received on Fri Aug 12 2016 - 11:00:03 PDT
