Thanks a lot. On Fri, Jun 18, 2010 at 9:30 AM, Justin A. Lemkul <jalem...@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.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. >> >> >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@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-requ...@gromacs.org >> <mailto:gmx-users-requ...@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 > > ======================================== > > -- > gmx-users mailing list gmx-users@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 the www interface > or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Aswathy
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