[gmx-users] removing number of sol

[gromacs query]

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:

>>>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 <erikm at 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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