[gmx-users] removing number of sol

[gromacs query]

Dear Erik,

I am new to Gromacs and used AMBER before, and I am exploring various
options in GROMACS too. Surely I will look in to g_select. Also as I was
using sed, one should include an extra space (using vi) in gro file just
before residue number and then can use sed to remove like this: sed -e '/
35SOL/d' -e '/ 36SOL/d' -e '/ 38SOL/d' -e '/ 39SOL/d' old.gro > new2.gro

But please note I included an extra space / 35SOL/d (instead of /35SOL/d)
by this sed will remove 35SOL not 135SOL.

regards,


On Fri, Mar 1, 2013 at 5:27 PM, Erik Marklund <erikm at xray.bmc.uu.se> wrote:

> 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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