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

Anirban Ghosh anirbanz83 at yahoo.co.in
Thu May 14 11:31:07 CEST 2009


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.


 Anirban GhoshGrade Based Engineer
Bioinformatics Team
Centre for Development of Advanced Computing (C-DAC)
Pune, India

      From Chandigarh to Chennai - find friends all over India. Go to http://in.promos.yahoo.com/groups/citygroups/
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