[gmx-users] Remove water molecules from .tpr file

John Whittaker johnwhittake at zedat.fu-berlin.de
Mon Jan 27 18:15:30 CET 2020


Hi Navneet,

You can probably delete the water molecules and ions from your .gro file
and run all the necessary files through grompp again.

This should generate a new dummy .tpr file you can use that matches your
trajectory file.

Best,

John

> Hello Everyone!
>
> I want to calculate the g_mmpbsa (binding free energy) for a
> protein+ligand
> complex.
> I want to delete the water molecules and other ions from the system.
> I have removed the water molecules from the .xtc file. But how to
> manipulate and remove the water molecules information from .tpr
> (md_0_10.tpr)file. I want a new .tpr file which matches my new trajectory
> file. How to do this?
>
> Regards
> Navneet
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