[gmx-users] removing number of sol

[Erik Marklund]

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  
>> <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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>>>
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