If you have a pdb file instead of a gro file then e.g. pymol might be
useful.
Erik
On Mar 2, 2013, at 2:01 PM, gromacs query wrote:
Dear Erik,
I am new to Gromacs and used AMBER before, and I am exploring various
options in GROMACS too. Surely I will look in to g_select. Also as I
was
using sed, one should include an extra space (using vi) in gro file
just
before residue number and then can use sed to remove like this: sed -
e '/
35SOL/d' -e '/ 36SOL/d' -e '/ 38SOL/d' -e '/ 39SOL/d' old.gro >
new2.gro
But please note I included an extra space / 35SOL/d (instead of /
35SOL/d)
by this sed will remove 35SOL not 135SOL.
regards,
On Fri, Mar 1, 2013 at 5:27 PM, Erik Marklund <er...@xray.bmc.uu.se>
wrote:
Hi,
Then the problem lies in automating what molecules are to be removed,
right? Try g_select or look into trjorder.
Erik
On Mar 1, 2013, at 2:45 PM, gromacs query wrote:
Aha! thanks Erik (and Justin),
I really feel sorry 35 and 135 will be removed by sed. I must have
given a
thought about that. So this was reason sed was over doing the
things. Also
as you asked: They are random residue number water molecules so
not continuous and they were selected on the criteria based on X Y Z
coordinates (some space fixed and outlier waters are to be removed)
regards,
On Fri, Mar 1, 2013 at 3:09 PM, Erik Marklund <er...@xray.bmc.uu.se>
wrote:
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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