[gmx-users] Enough hydration of the channel

[Aswathy]

Thanks a lot.

On Fri, Jun 18, 2010 at 9:30 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Aswathy wrote:
>
>> Thank you very much.
>>
>> In some papers I have seen the graph for hydration of the channel. How can
>> we calculate that using Gromacs ? (or any other program?)
>>
>
> Have a look at some of Oliver Beckstein's programs:
>
> http://sbcb.bioch.ox.ac.uk/oliver/software/
>
> There are several that might be useful to you.
>
> -Justin
>
>
>> Regards,
>> -Aswathy
>>
>>
>>
>> On Thu, Jun 17, 2010 at 7:52 PM, <chris.neale at utoronto.ca <mailto:
>> chris.neale at utoronto.ca>> wrote:
>>
>>    Determining how many waters is sufficient is a tough problem, try
>>    successive runs of option #3, below. As for the simpler topic of
>>    getting more hydration:
>>
>>    1. If the issue is simply getting the channel hydrated enough to
>>    overcome some transition from dry to wet, then run a neat water box
>>    od 216 spc for 100 ps and extract a frame every 10 ps, then run
>>    genbox 10x successively using each of these frames. This should give
>>    you massive hydration.
>>
>>    2. If that doesn't work, then you could add a new equilibration step
>>    where you posres some cap waters so that the channel can not dry
>>    out. This may allow SC's to equilibrate to a wet environment.
>>
>>    3. If the issue is that the water is still moving out, then why not
>>    do SMD on a water into the pore and find out where the repulsion is.
>>
>>    -- original message --
>>
>>    Hi everyone,
>>
>>    I have a homology model of a transporter. I want to study the ligand
>>    transport through the channel. i have done the following steps.
>>
>>    1. Ligand has docked to the mouth of the channel
>>    2.  Inserted the complex in POPC bilayer, then solvated, and
>>    equilibrated
>>    for 4ns(with position restarint on Protein & ligand)
>>    3. Then I saw tht there are very few wtaer inside the pore, Since this
>>    channel is an aqueous pore, I have added water to the channel using
>>    genbox.
>>    4. Then the complete system equilibrated for pico seconds.
>>    5,in order to select different snap shots for SMD (want to do a
>> multiple
>>    SMDs with different starting structures.) I have run 1ns Production
>>    run and
>>    selected different frames.
>>
>>    Suddenly I found that still there is no enough water in the pore,
>>    the water
>>    is moving away from the channel during step 4 &5?
>>
>>    How can I solve this problem? Also how will I know how many water
>>    molecules
>>    will be sufficient for the channel?
>>
>>    Thanks for your support.
>>
>>
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>>
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>>
>>
>>
>> --
>> Aswathy
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
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-- 
Aswathy
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