[gmx-users] waters in ion channels

[Nicolas SAPAY]

Hello,

If you simply need to remove water molecules, you can simply use VMD,
Pymol or whatever allows you to select and save atom coordinates in a
format readable by gromacs. In VMD, I would do something like:
     set sel [atomselect top "not (same resid as (water within 5 of
resname DPPC)"]

or
     set sel [atomselect top "not (water and same resid as (z>20 and z>80))"]

then
     animate write pdb myfile.pdb sel $sel

That will select and save  in a pdb file all but the water molecules too
close to the lipids.

Nicolas

>
>
> --- On Fri, 3/7/09, Itamar Kass <itamar.kass at gmail.com> wrote:
>
> From: Itamar Kass <itamar.kass at gmail.com>
> Subject: Re: [gmx-users] waters in ion channels
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Date: Friday, 3 July, 2009, 3:42 PM
>
> Hi,
>
> I would say that those are water molecule which enter from the bulk
> water. This is normal and probably important for the physiological
> function of the system.
>
> Best,
> Itamar
>
> thank you a lot for the answar. one thing i would like to ask again that
> how can i be sure that those water molecules are not inside the 
> hydrophobic core? and if they are not how deleting them could affect the
> system?
> thanks again....
> Shamik
>
>
>
>
>
>
>
> On Fri, Jul 3, 2009 at 8:08 PM, Samik Bhattacharya<samikbhat at yahoo.co.in>
> wrote:
>> hi i'm simulating a ion channel protein in DPPC membrane. i'm following
>> Justin's tutorial for that. and have completed upto the solvation step.
>> but
>> right after solvation, i found some water molecules in the channel. now
>> i
>> want to delete those molecules. in the tutorial it is advised tyo use
>> the
>> keepbyz script to do that.. but after using that i didn't find any
>> change
>> in the structure. watres are still present in there. may be i am making
>> some
>> mistake in running the program or something like that!!! can anyone
>> suggest
>> any thing to solve the problem...thanking you all in advance.
>>
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[ Nicolas Sapay - Post-Doctoral Fellow ]
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