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
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> 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
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Received on Fri Aug 12 2016 - 00:30:02 PDT
