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 >
new_system.gro
the last last step is " editconf -f new_system.gro -o
new_system_sequential_nubers.gro
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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