nitu sharma wrote:
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
Thus new_system.gro is inconsistent. Look at the three contributing .gro
files, and the resulting .gro file. Pay attention to the line early on
that specifies how many atoms are in the file, and that this is right,
and that there is a box specification at the end.
Mark
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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