Dear Dr. Elvis,
I tried your suggestion of creating receptor and ligand prmtops from the
complex_gas.prmtop using the ante-MMPBSA.py as well as doing new
topologies.
For the use of ante-MMPBSA.py, files are created but when I run the
MMPBSA.py, the error comes
................................................................
File "/mnt/d/amber18//bin/MMPBSA.py", line 98, in <module>
app.loadcheck_prmtops()
File "/mnt/d/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 611, in loadcheck_prmtops
self.normal_system.CheckConsistency()
File
"/mnt/d/amber18/lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py",
line 905, in CheckConsistency
raise PrmtopError('Topology files have inconsistent RADIUS_SETs')
PrmtopError: Topology files have inconsistent RADIUS_SETs
....................................
I am using --radii=mbondi3 when I used the ante-MMPBSA and earlier had used
the set default PBRadii mbondi3 when creating topologies in tleap as I am
using igb=8 in the MMPBSA.py input file.
In case I dont use the --radii command in the ante-MMPBSA, the error is s
follows
---------------------------------------------------------------------------
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /mnt/d/amber18/bin/mmpbsa_py_energy
cpptraj found! Using /mnt/d/amber18/bin/cpptraj
mmpbsa_py_nabnmode found! Using /mnt/d/amber18/bin/mmpbsa_py_nabnmode
Preparing trajectories for simulation...
1000 frames were processed by cpptraj for use in calculation.
4 frames were processed by cpptraj for nmode calculations.
Running calculations on normal system...
Beginning GB calculations with /mnt/d/amber18/bin/mmpbsa_py_energy
calculating complex contribution...
Atom 19 outside the allowed range of 1-2 Angstroms for igb==7.
... regenerate prmtop with 'bondi' radii! File
"/mnt/d/amber18//bin/MMPBSA.py", line 100, in <module>
app.run_mmpbsa()
File "/mnt/d/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/mnt/d/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/mnt/d/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 157, in run
self.prmtop))
CalcError: /mnt/d/amber18/bin/mmpbsa_py_energy failed with prmtop
complex_gas.prmtop
-----------------------------------------------------------------------------
In case I create new topologies, error comes for the difference in atom
numbers.
Is there any other way to solve the matter?
Thank you
Regards
On Sun, Feb 28, 2021 at 7:02 PM Elvis A F Martis <martiseaf.elvismartis.in>
wrote:
> Hi
> The total number of atoms in receptor.prmtop and hpr.prmtop do not add up
> to the number of atoms in complex_gas.prmtop. the difference is just 1.
> You can either build the gas topologies again or use ante-MMPBSA.py on the
> complex_gas.prmtop to save receptor and ligand topologies
>
> On Sun, 28 Feb 2021 at 15:26, Ayesha Fatima <ayeshafatima.69.gmail.com>
> wrote:
>
> > Dear Dr. Elvis,
> > Files are attached hpr is the ligand. I can see that the number of water
> > molecules differs even from the pdb file I created when i solvated the
> > complex. Not sure what happened along the way. should I continue to make
> a
> > new trajectory for calculating the mmgbsa?
> > Thank you
> > Regards
> >
> > complex_gas.prmtop
> > <
> >
> https://drive.google.com/file/d/1qlD6bLMFhOKTddlswJcyJoqfv-A7Z5VV/view?usp=drive_web
> > >
> > complex_solv.prmtop
> > <
> >
> https://drive.google.com/file/d/1HU6122WVEBGxCPQa7QNcAU0wKI3QVXf3/view?usp=drive_web
> > >
> > frame1-3.pdb
> > <
> >
> https://drive.google.com/file/d/1j8VejBB-47JjTAnbtHX3XnmFNm8YE8Sq/view?usp=drive_web
> > >
> > hpr.prmtop
> > <
> >
> https://drive.google.com/file/d/11gpiLGEo_zkdgwtQI1AfgJMJlQe5QjsR/view?usp=drive_web
> > >
> > receptor_gas.prmtop
> > <
> >
> https://drive.google.com/file/d/1fbjCA-NEv4WpEIYZ_kU7Q2uV6_9wZR8f/view?usp=drive_web
> > >
> > lvis,
> >
> >
> > On Sun, Feb 28, 2021 at 3:07 PM Elvis A F Martis <
> martiseaf.elvismartis.in
> > >
> > wrote:
> >
> > > Can you send me all the prmtop files and 1-3 frames from the trajectory
> > off
> > > the list?
> > >
> > > On Sunday, 28 February 2021, Ayesha Fatima <ayeshafatima.69.gmail.com>
> > > wrote:
> > >
> > > > Dear Dr. Elvis,
> > > > Sorry for the late reply. Yes after stripping water, the trajectory
> is
> > > > accepted by the cpptraj and I can get the rmsd plot. however cannot
> get
> > > the
> > > > histogram to appear. will check again. but MMPBSA is still not
> > happening.
> > > >
> > > > Thank you
> > > > Regards
> > > >
> > > > On Sat, 27 Feb 2021, 7:26 pm Elvis A F Martis, <
> > martiseaf.elvismartis.in
> > > >
> > > > wrote:
> > > >
> > > > > After stripping water from the trajectories, are you able to
> > > > > able load the trajectory using the dry complex.prmtop in cpptraj?
> > > > >
> > > > >
> > > > > On Saturday, 27 February 2021, Ayesha Fatima <
> > > ayeshafatima.69.gmail.com>
> > > > > wrote:
> > > > >
> > > > > > Dear Dr. Elvis,
> > > > > > Thank you for your response.
> > > > > > I am passing all topologies as indicated in the manual
> > > > > > 1 solvated is the same used for the simulation
> > > > > > 3 unsolvated 1 each for complex, receptor and ligand
> > > > > > Thank you
> > > > > > Regards
> > > > > >
> > > > > > On Sat, 27 Feb 2021, 5:47 pm Elvis A F Martis, <
> > > > martiseaf.elvismartis.in
> > > > > >
> > > > > > wrote:
> > > > > >
> > > > > > > if you are directly passing the solvated trajectory to
> MMPBSA.py,
> > > > don't
> > > > > > > forget to use -sp <solvated_trajectory>.prmtop
> > > > > > >
> > > > > > > On Saturday, 27 February 2021, Ayesha Fatima <
> > > > > ayeshafatima.69.gmail.com>
> > > > > > > wrote:
> > > > > > >
> > > > > > > > Dear all,
> > > > > > > > I have a query regarding the above subject.
> > > > > > > > I prepared my solvated and unsolvated complex and other
> > required
> > > > > files
> > > > > > > for
> > > > > > > > simulation. the simulation ran fine. Now when i want to
> > calculate
> > > > the
> > > > > > > > mmpbsa, the error comes for the difference in number of atoms
> > > > between
> > > > > > > > topology and trajectory files. my simulation generated the
> .nc
> > > > > > trajectory
> > > > > > > > and used the MMPBSA.py script for calculation. I have started
> > the
> > > > > > > > simulation again but it will take some time now.
> > > > > > > > Is there a workaround?
> > > > > > > > Thank you
> > > > > > > > Regards
> > > > > > > > _______________________________________________
> > > > > > > > AMBER mailing list
> > > > > > > > AMBER.ambermd.org
> > > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > > >
> > > > > > > _______________________________________________
> > > > > > > AMBER mailing list
> > > > > > > AMBER.ambermd.org
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> > > > > > >
> > > > > > _______________________________________________
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> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >
> > > > >
> > > > >
> > > > > --
> > > > > Best Regards
> > > > > Elvis
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
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> > > > AMBER.ambermd.org
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> > > >
> > >
> > >
> > > --
> > > Best Regards
> > > Elvis
> > > _______________________________________________
> > > 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
> >
>
>
> --
> Best Regards
> Elvis
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>
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Received on Sun Feb 28 2021 - 09:00:02 PST
