[gmx-users] removing number of sol

[Justin Lemkul]

On 3/1/13 7:58 AM, 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:
>
>>>> 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 .
>

I don't know about editconf, but trjconv can do this.

-Justin

>
> 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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-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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