It is tough to point out what might have gone wrong.
However, for mmgbsa calculations, I prepare all topology files at once in
leap by loading ligand and receptor coordinates separately and then
combining them using leap. This way, I always keep know that natoms in
complex.prmtop = receptor.prmtop + ligand.prmtop.
On Mon, 8 Mar 2021 at 00:23, Ayesha Fatima <ayeshafatima.69.gmail.com>
wrote:
> Dear Dr. Elvis,
> I tried the ante-MMPBSA.py again with 1 change
> 1. --radii=mbondi2
> it created the files and the receptor topology had 4941 atoms. this is 1
> atom more than my previous files. So the total atoms in the unsolvated
> complex totalled nicely when receptor and ligand atoms were added.
>
> The second change I did was as you had suggested. in the script file, i
> changed igb=5
> The calculation is running now. have to see if any error comes in.
>
> but I still dont understand what happened? Why I got less atoms when i
> prepared previously? I prepared other complexes and their atoms add up
> correctly.
>
> Thank you for your prompt responses.
>
> Regards
>
>
> the other change that I
>
>
>
> On Mon, Mar 1, 2021 at 2:10 PM Elvis A F Martis <martiseaf.elvismartis.in>
> wrote:
>
> > Hi
> > try using igb=5
> >
> > On Mon, 1 Mar 2021 at 00:14, Ayesha Fatima <ayeshafatima.69.gmail.com>
> > wrote:
> >
> > > 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
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> > > > > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > > > > >
> > > > > > > > > _______________________________________________
> > > > > > > > > AMBER mailing list
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> > > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > --
> > > > > > > > Best Regards
> > > > > > > > Elvis
> > > > > > > > _______________________________________________
> > > > > > > > AMBER mailing list
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> > > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > > >
> > > > > > > _______________________________________________
> > > > > > > AMBER mailing list
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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
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > 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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>
--
Best Regards
Elvis
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Received on Sun Mar 07 2021 - 21:30:02 PST
