AMBER Archive (2009)

Subject: Re: [AMBER] Solvating the interior of a channel

From: Daniel Smith (das92amber_at_gmail.com)
Date: Fri Feb 13 2009 - 15:02:24 CST

Thanks. I will try those suggestions and see what works.

On Wed, Feb 11, 2009 at 11:04 AM, Jason A. Ford-Green <jgreen_at_ccmsi.us>wrote:

>
> I have never used the plugin, but I see VMD has a script called Dowser
> that, like the below two programs, finds cavities and solvates them
> considering energetically favorable solvation states. Hope this helps!
>
> Cheers,
>
> Jason Ford-Green
>
> ---------- Original Message ----------------------------------
> From: Shozeb Haider <shozeb.haider_at_pharmacy.ac.uk>
> Reply-To: AMBER Mailing List <amber_at_ambermd.org>
> Date: Wed, 11 Feb 2009 13:15:07 +0000
>
> >Try looking at the programs VOIDOO (looks for cavities) and FLOOD
> >(floods the cavities with solvent).
> >
> >Best wishes
> >
> >Shozeb
> >
> >
> >
> >Daniel Smith wrote:
> >> Hello,
> >>
> >> I am currently running Amber 9 but also have access to Amber 10 if need
> be.
> >> I have a channel protein that I am trying to simulate in vacuo. However,
> I
> >> would like to solvate the interior of the channel. How might I go about
> >> doing this other than placing the waters in there individually? I have
> tried
> >> solvating the protein, but that gives me thousands of unnecessary
> waters.
> >>
> >> Thank you,
> >> Daniel Smith
> >> _______________________________________________
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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >
> >
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>
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