[gmx-users] removal of unwanted water from hydrphobic core of lipid

nitu sharma sharmanitu35 at gmail.com
Thu May 28 12:00:42 CEST 2009

Dear all,

                     I want to remove unwanted water molecules from
hydrophobic core of lipid of solvated.gro file . For this I am using
keepbyz.pl script of chris neale  .
After the step " cat not_last_line.gro  new_waters.gro last_line.gro >
the last last step is " editconf -f new_system.gro -o

in this step in last file water molecules unable to added  editconf only
read the lipid and protein molecule.
the warning shows in editconf step is-
WARNING 1 [file aminoacids.dat, line 1]:
  Bad box in file new_system.gro

Generated a cubic box   12.416 x   15.565 x   14.988
Read 15422 atoms
Volume: 2896.51 nm^3, corresponds to roughly 1303400 electrons
No velocities found

note:- as initial .gro file I have used boxed.pdb ( before solvation file).
If anybody have some idea please suggest me something.

thank you very much in advance.

nitu sharma.
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