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
> > > 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Feb 27 2021 - 23:00:02 PST
