[gmx-users] removing number of sol

[Erik Marklund]

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 <erikm at 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  
>>>> <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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