AMBER Archive (2009)

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

From: Jason A. Ford-Green (jgreen_at_ccmsi.us)
Date: Wed Feb 11 2009 - 10:04:24 CST

 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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>>
>>
>
>
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