Thanks a lot.<br><br><div class="gmail_quote">On Fri, Jun 18, 2010 at 9:30 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
<br>
Aswathy wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thank you very much.<br>
<br>
In some papers I have seen the graph for hydration of the channel. How can we calculate that using Gromacs ? (or any other program?)<br>
</blockquote>
<br></div>
Have a look at some of Oliver Beckstein's programs:<br>
<br>
<a href="http://sbcb.bioch.ox.ac.uk/oliver/software/" target="_blank">http://sbcb.bioch.ox.ac.uk/oliver/software/</a><br>
<br>
There are several that might be useful to you.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Regards,<br>
-Aswathy<div><div></div><div class="h5"><br>
<br>
<br>
On Thu, Jun 17, 2010 at 7:52 PM, <<a href="mailto:chris.neale@utoronto.ca" target="_blank">chris.neale@utoronto.ca</a> <mailto:<a href="mailto:chris.neale@utoronto.ca" target="_blank">chris.neale@utoronto.ca</a>>> wrote:<br>
<br>
Determining how many waters is sufficient is a tough problem, try<br>
successive runs of option #3, below. As for the simpler topic of<br>
getting more hydration:<br>
<br>
1. If the issue is simply getting the channel hydrated enough to<br>
overcome some transition from dry to wet, then run a neat water box<br>
od 216 spc for 100 ps and extract a frame every 10 ps, then run<br>
genbox 10x successively using each of these frames. This should give<br>
you massive hydration.<br>
<br>
2. If that doesn't work, then you could add a new equilibration step<br>
where you posres some cap waters so that the channel can not dry<br>
out. This may allow SC's to equilibrate to a wet environment.<br>
<br>
3. If the issue is that the water is still moving out, then why not<br>
do SMD on a water into the pore and find out where the repulsion is.<br>
<br>
-- original message --<br>
<br>
Hi everyone,<br>
<br>
I have a homology model of a transporter. I want to study the ligand<br>
transport through the channel. i have done the following steps.<br>
<br>
1. Ligand has docked to the mouth of the channel<br>
2. Inserted the complex in POPC bilayer, then solvated, and<br>
equilibrated<br>
for 4ns(with position restarint on Protein & ligand)<br>
3. Then I saw tht there are very few wtaer inside the pore, Since this<br>
channel is an aqueous pore, I have added water to the channel using<br>
genbox.<br>
4. Then the complete system equilibrated for pico seconds.<br>
5,in order to select different snap shots for SMD (want to do a multiple<br>
SMDs with different starting structures.) I have run 1ns Production<br>
run and<br>
selected different frames.<br>
<br>
Suddenly I found that still there is no enough water in the pore,<br>
the water<br>
is moving away from the channel during step 4 &5?<br>
<br>
How can I solve this problem? Also how will I know how many water<br>
molecules<br>
will be sufficient for the channel?<br>
<br>
Thanks for your support.<br>
<br>
<br>
-- gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br></div></div>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><div class="im"><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before<br>
posting!<br>
Please don't post (un)subscribe requests to the list. Use thewww<br>
interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br></div>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>.<div class="im"><br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br>
<br>
<br>
<br>
-- <br>
Aswathy<br>
<br>
</div></blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<div class="im"><br>
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br></div>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<div><div></div><div class="h5">
<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>Aswathy<br>