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
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Received on Fri Aug 12 2016 - 12:00:03 PDT
