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
>> _______________________________________________
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>>
>
>
>
> --
> 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 - 11:00:03 PDT
