[gmx-users] Re: how to g_select bound water molecules

[Yun Shi]

OK. I have a protein "ab" and ligand "lig", and I want to select the bound
water between them. So I used

g_select -f trajout.xtc -s mdrun.tpr -n index.ndx -select '"boundwaters"
resname SOL and within 0.4 of group "ab" and within 0.4 of group "lig"' -on
boundwaters.ndx

Then I can use the ndx file to do other things. The hard part is what after
-select


On Mon, Apr 2, 2012 at 5:11 PM, Dallas Warren <Dallas.Warren at monash.edu>wrote:

>  For future reference of others that may struggle with g_select, it would
> be a very good idea for you to put on the emailing list how you achieved it.
> ****
>
> ** **
>
> Catch ya,
>
> Dr. Dallas Warren****
>
> Medicinal Chemistry and Drug Action****
>
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at monash.edu****
>
> +61 3 9903 9304
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a
> nail. ****
>
> ** **
>
> *From:* gmx-users-bounces at gromacs.org [mailto:
> gmx-users-bounces at gromacs.org] *On Behalf Of *Yun Shi
> *Sent:* Tuesday, 3 April 2012 9:58 AM
> *To:* Discussion list for GROMACS users
> *Subject:* [gmx-users] Re: how to g_select bound water molecules****
>
> ** **
>
> Never mind. I got it.****
>
> On Mon, Apr 2, 2012 at 4:20 PM, Yun Shi <yunshi09 at gmail.com> wrote:****
>
> Hello all,
>
> Can anyone tell me how to get in "help examples" in g_select by typing
> some commands?
>
> Anyway, I want to select bound waters between my ligand and protein using
> -select 'resname SOL & within 0.5 ...'. Any idea?
>
> Thanks for any suggestion.
>
> Yun****
>
> ** **
>
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