[gmx-users] removing number of sol

[Erik Marklund]

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?

>
>>>> 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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