[gmx-users] removing number of sol

Erik Marklund erikm at xray.bmc.uu.se
Fri Mar 1 13:48:09 CET 2013


The ndx format is really simple. You can easily script your way to a  
new index group as long as the selection of atoms can be automated.  
Furthermore, the gro format is also simple, so you can filter out the  
unwanted residues there instead of using an index file.

Erik

On Mar 1, 2013, at 1:42 PM, gromacs query wrote:

> Dear All,
>
> I know the residue numbers of SOL molecules (which are more than  
> thousands)
> which I want to remove them from a gro file. I searched that  
> make_ndx can
> be used make a index file to define residues. But It is a prompt  
> based tool
> and its difficult to type manually thousands of residue numbers.
>
> 1) Is there some way to feed the residue numbers to make_ndx? Or I  
> need to
> make index file format my self by some scritpting Or is there is  
> rather
> easier way of doing in gromacs.
>
> 2) Also is there any direct command which helps to remove a residue  
> number
> directly from a gro file without using index file input; means residue
> defined in command itself?
>
> 3) Also once I get index file can editconf help to write a new gro  
> without
> the residues mentioned in index file?. I used this editconf -f  
> my.gro -n
> index.ndx -o del.gro .
>
> This gave me del.gro having residues mentioned in index file. But I  
> want
> del.gro file without the residues mentioned in index file.
>
>
> regards,
> -- 
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