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 Sat Feb 27 2021 - 23:30:02 PST
