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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>
>
> --
> Best Regards
> Elvis
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Received on Sun Feb 28 2021 - 02:00:02 PST
