[gmx-users] removing number of sol

Erik Marklund erikm at xray.bmc.uu.se
Sat Mar 2 18:40:52 CET 2013 

If you have a pdb file instead of a gro file then e.g. pymol might be  
useful.

Erik

On Mar 2, 2013, at 2:01 PM, gromacs query wrote:

> 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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