On Mar 1, 2013, at 2:08 PM, Erik Marklund wrote:
On Mar 1, 2013, at 1:58 PM, gromacs query wrote:
Dear Erik,
so you can filter out the unwanted residues there instead of
using an
index file.
There are thousands of water to be removed so simple commands like
sed
exhausts when I run it in loops. e.g. Just to say :
sed -e '/35SOL/d' -e '/36SOL/d' -e '/38SOL/d' -e '/39SOL/d' -e '/
40SOL/d'
-e '/41SOL/d' -e '/42SOL/d' -e '/43SOL/d' -e '/44SOL/d' -e '/45SOL/d'
old.gro > new2.gro
this will remove such 10 residues but if you run this again and
again (in
text exe format) say 1000 times it exhausts some how and remove
waters
which are not even mentioned in sed command! I have checked it many
times.
So I thought if index file could help me. But please reply for
point 3:
First of all, that's not a safe way of removing waters. Note that
both SOL 35, SOL 135, ... will be removed by that command. Secondly,
I'm sure you can think of a better way of scripting it, using e.g.
sed or awk. By which criteria do you select the waters to be removed?
If its a contiguous chunk then it's dead simple.
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 .
thanks,
This gave me del.gro having residues mentioned in index file. But I
want
del.gro file without the residues mentioned in index file.
On Fri, Mar 1, 2013 at 2:48 PM, Erik Marklund
<er...@xray.bmc.uu.se> wrote:
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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