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
Received on Sat Feb 27 2021 - 03:00:02 PST
