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.ne...@utoronto.ca
<mailto:chris.ne...@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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--
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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