Just an update. I tried using Dowser (I installed the program itself) which
put seemingly random waters into the folds of the protein. Flood (in
conjunction) with Voidoo worked absolutely brilliantly. The atoms seemed to
fill the channel quite well, and it's output was a pdb file with O atoms in
WAT residues which Amber read easily.
Thanks,
Daniel Smith
On Fri, Feb 13, 2009 at 4:02 PM, Daniel Smith <das92amber.gmail.com> wrote:
> Thanks. I will try those suggestions and see what works.
>
>
> On Wed, Feb 11, 2009 at 11:04 AM, Jason A. Ford-Green <jgreen.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.pharmacy.ac.uk>
>> Reply-To: AMBER Mailing List <amber.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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>
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Received on Mon Feb 16 2009 - 01:12:09 PST
