I received the following error when removing the -sp input:
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 186, in make_trajectories
ligtraj.Setup(INPUT['startframe'],INPUT['endframe'],INPUT['interval'])
File "/N/soft/rhel6/amber/intel/mpi/14/amber14/lib/python2.7/
site-packages/MMPBSA_mods/make_trajs.py", line 503, in Setup
(startframe, self.total_frames))
TrajError: start frame (20000) > total frames (4595)
Error occured on rank 0.
Exiting. All files have been retained.
with:
###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 -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
~
On Mon, Aug 22, 2016 at 11:54 AM, JoAnne Babula <jbabula.umail.iu.edu>
wrote:
> Per the original command line in Amber tutorial 3 section 3.3, -sp input
> calls for the solvated top of the complex.
> $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -sp ras-raf_solvated.prmtop -cp
> rasraf.prmtop -rp ras.prmtop -lp raf.prmtop -y *.mdcrd -mc
> rasraf_mutant.prmtop -mr ras_mutant.prmtop
>
> from: http://ambermd.org/tutorials/advanced/tutorial3/
> py_script/section3.htm
> The -cp input is the complex with solvate removed. I will attempt to run
> the job without the -sp input if you think that will solve the issue.
>
>
>
> On Mon, Aug 22, 2016 at 11:38 AM, Nhai <nhai.qn.gmail.com> wrote:
>
>>
>> No I meant that in the command line.
>>
>> Hai
>>
>> > On Aug 22, 2016, at 11:33 AM, JoAnne Babula <jbabula.umail.iu.edu>
>> wrote:
>> >
>> > Hello Nhai,
>> >
>> > The solvated top are per request of Bilal:
>> >
>> > 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.
>> >
>> >
>> >
>> > I am assuming he is going to run a strip on the water himself and try
>> to re
>> > produce my error message.
>> >
>> >> On Mon, Aug 22, 2016 at 11:31 AM, Nhai <nhai.qn.gmail.com> wrote:
>> >>
>> >> All of you trajectories are nowat, so what is GRL_INO_solvate.top for?
>> >>
>> >> Hai
>> >>
>> >>>> On Aug 22, 2016, at 10:19 AM, JoAnne Babula <jbabula.umail.iu.edu>
>> >>> wrote:
>> >>>
>> >>> 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-MMPB
>> SA.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
>> >>
>> >> _______________________________________________
>> >> 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
>>
>
>
>
> --
> 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
Received on Mon Aug 22 2016 - 09:30:02 PDT
