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
> > > > > > > _______________________________________________
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> > > >
> > > >
> > > > --
> > > > Best Regards
> > > > Elvis
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> >
> > --
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> > Elvis
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Best Regards
Elvis
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Received on Sun Feb 28 2021 - 03:30:02 PST
