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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