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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Received on Sat Feb 27 2021 - 03:30:02 PST
