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-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
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Received on Mon Aug 22 2016 - 09:00:02 PDT
