[gmx-users] Enough hydration of the channel
Justin A. Lemkul
jalemkul at vt.edu
Fri Jun 18 06:00:18 CEST 2010
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.
>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list. Use thewww
> interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>
>
> --
> 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
========================================
More information about the gromacs.org_gmx-users
mailing list