Re: [AMBER] counterions present in topology files for the MMPSA calculation

From: Elvis Martis <>
Date: Wed, 5 Feb 2020 19:21:33 +0530

You can parmed to delete those ions and save new prmtop and rst file

On Wednesday, February 5, 2020, Shilpa Gupta <>

> Dear Amber Users,
> For MMPBSA run, i am generating the individual topology file of complex,
> receptor , and ligand using 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
AMBER mailing list
Received on Wed Feb 05 2020 - 06:00:04 PST
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