Hi Bilal,
I have attempted to run the free energy calculation with your suggestions
and received the following error messages:
1. With serial MMPBSA.py:
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: 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'.
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'.
Error: Could not set up GRL_INO_nowat.mdcrd for reading.
Error: Could not set up input trajectory 'GRL_INO_nowat.mdcrd'.
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", line 103,
in <module>
"/N/soft/rhel6/amber/intel/mpi/14/amber14/bin/MMPBSA.py", line 103, in
<module>
File "/N/soft/rhel6/amber/intel/mpi/14/amber14/bin/MMPBSA.py", 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
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
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
File "/N/soft/rhel6/amber/intel/mpi/14/amber14/bin/MMPBSA.py", 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
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
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
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
Exiting. All files have been retained.
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
Exiting. All files have been retained.
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
Exiting. All files have been retained.
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
Exiting. All files have been retained.
and the input file being:
###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 -O -i mmpbsa.in -o pbsa_karst.dat -sp
../../../../../INO/sim1/PREP/GRL_INO_solvate.top -cp top/GRL_INO_nowat.top
-rp top/native_nowat.top -lp top/LINO_nowat.top -y GRL_INO_nowat.mdcrd -yr
native_nowat.mdcrd -yl LINO_nowat.mdcrd >progress
~
2. With smaller mdcrd files of 20,000 frames instead of 120,000:
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 76, in make_trajectories
raise MMPBSA_Error('Must have at least as many frames as processors!')
MMPBSA_Error: Must have at least as many frames as processors!
Error occured on rank 0.
Exiting. All files have been retained.
On Sat, Aug 13, 2016 at 4:11 AM, Bilal Nizami <nizamibilal1064.gmail.com>
wrote:
> JoAnne,
>
> Can you attach your solvated prmtop, so that I can check if i can reproduce
> the error? How big is your trajectory? is it possible to try it with few
> frames only. Or try the same step with serial version of mmpbsa.py, see if
> the issue is resolved.
>
> Regards,
>
> 2016-08-12 20:49 GMT+02:00 Hai Nguyen <nhai.qn.gmail.com>:
>
> > you can try to follow old thread first.
> >
> > https://www.google.com/search?q=expect+only+3+or+6+box+
> > coords&ie=utf-8&oe=utf-8#q=expect+only+3+or+6+box+coords&tbas=0
> >
> > PS: You should always use netcdf format.
> >
> > Hai
> >
> > On Fri, Aug 12, 2016 at 2:41 PM, JoAnne Babula <jbabula.umail.iu.edu>
> > wrote:
> >
> > > Okay, my apologies, I have no re-run the script with the @ designation
> > and
> > > produced the 3 respective topologies. However, I still received the
> same
> > > error concerning the box coordinates:
> > >
> > > 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.
> > >
> > >
> > > Any other ideas?
> > >
> > >
> > > On Fri, Aug 12, 2016 at 1:38 PM, JoAnne Babula <jbabula.umail.iu.edu>
> > > wrote:
> > >
> > > > The ligand is atoms 3135-3213. Water is 3124-39717.
> > > >
> > > > On Fri, Aug 12, 2016 at 1:34 PM, JoAnne Babula <jbabula.umail.iu.edu
> >
> > > > wrote:
> > > >
> > > >> 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
> > > >>
> > > >
> > > >
> > > >
> > > > --
> > > > Very Respectfully,
> > > >
> > > > JoAnne J Babula
> > > > Ph.D. Candidate, IUSM, Dept. of Pharmacology
> > > > U.S. Army, 1LT, MS
> > > >
> > >
> > >
> > >
> > > --
> > > 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Aug 22 2016 - 07:30:02 PDT
