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
usi
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
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 ab
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
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
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 '/3
On 3/1/13 7:58 AM, 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'
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
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 1:4
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 number
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