[gmx-users] Enough hydration of the channel
Justin A. Lemkul
jalemkul at vt.edu
Fri Jun 18 06:00:18 CEST 2010
> 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:
There are several that might be useful to you.
> 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
> 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
> 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
> will be sufficient for the channel?
> Thanks for your support.
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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