Dear all,<br><br> 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 .<br>After the step " cat not_last_line.gro new_waters.gro last_line.gro > new_system.gro <br>
the last last step is " editconf -f new_system.gro -o new_system_sequential_nubers.gro<br><br>in this step in last file water molecules unable to added editconf only read the lipid and protein molecule. <br>the warning shows in editconf step is-<br>
WARNING 1 [file aminoacids.dat, line 1]:<br> Bad box in file new_system.gro<br><br>Generated a cubic box 12.416 x 15.565 x 14.988<br>Read 15422 atoms<br>Volume: 2896.51 nm^3, corresponds to roughly 1303400 electrons<br>
No velocities found<br><br>note:- as initial .gro file I have used boxed.pdb ( before solvation file).<br>If anybody have some idea please suggest me something.<br><br>thank you very much in advance.<br><br>nitu sharma.<br>