You can parmed to delete those ions and save new prmtop and rst file
On Wednesday, February 5, 2020, Shilpa Gupta <guptashilpa0605.gmail.com>
wrote:
> Dear Amber Users,
> For MMPBSA run, i am generating the individual topology file of complex,
> receptor , and ligand using ante-MMPBSA.py from the solvated system. I have
> stripped the solvent as well as counterions but when i see the topology
> file of complex and ligand it contains counterions named as IM, which can
> not be recognised during MMPBSA run and error is coming. Is there any
> solution for the problem? Thanks in advance.
>
>
> Regards
> Shilpa
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>
--
Best Regards
Elvis Martis
Mumbai.
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Received on Wed Feb 05 2020 - 06:00:04 PST
