[gmx-users] removing number of sol

[gromacs query]

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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