[gmx-users] How to remove water from lipid bilayer core

Pawan Kumar pawan.chinari at gmail.com
Thu May 14 12:53:14 CEST 2009

Hello Anirban,

Greetings from Pawan.
You can find the scripts in this webiste :


On Thu, May 14, 2009 at 3:01 PM, Anirban Ghosh <anirbanz83 at yahoo.co.in>wrote:

> Hi ALL,
> I have a built a system of protein embeded in lipid bilayer and solvated it
> according to the GROMACS membrane simulation tutorial. I want to delete a
> few water molecules that are there in the hydrophobic core of the bilayer. I
> deleted them manually from the .gro file and corrected the atom numbers, but
> still getting an error:
> -----------------------------------------------------------------
> Invalid line in prt_genbox_MOD.gro for atom 73510:
>   10.81119  10.81119  10.01306
> -----------------------------------------------------------------
> How can I modify the last line and get a correct .gro file by removing the
> unwanted waters? In the tutorial it is stated that there are some scripts to
> remove the unwanted waters. Can anyone provide me such a script.
> Any suggestion is welcome.
> Regards,
> *Anirban Ghosh*
> *Grade Based Engineer
> Bioinformatics Team
> Centre for Development of Advanced Computing (C-DAC)
> Pune, India
> *
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