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

[Mark Abraham]

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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