Let me explain. Consider the channel of a membrane protein, r57 is a residue at the extracellular loop in this channel. I docked my ligand to the start of the channel. ie; just below the r57. (Here the I have not started from the solvent, but at the mouth of the channel , just below r 57..) Then I pulled the ligand through the channel(parameters as in the first mail). ie; pulled in such a way that, initially ligand was just below r57, then moved away from r57.
Plz check some data from the pullx file. 0.0000 7.74891 -0.754818 0.0200 7.74388 -0.754379 0.0400 7.73726 -0.752573 0.0600 7.73032 -0.756692 0.0800 7.72422 -0.747781 0.1000 7.72041 -0.754858 0.1200 7.71691 -0.744501 .............................................. .............................................. .............................................. 1099.8601 8.45571 5.46432 1099.8800 8.45551 -5.46076 1099.9000 8.45817 -5.46827 1099.9200 8.46075 5.46829 1099.9401 8.46317 -5.46782 1099.9601 8.46545 5.46577 1099.9801 8.46565 -5.47014 1100.0000 8.46651 5.46001 Thanks, Aswathy On Thu, Aug 5, 2010 at 4:28 PM, Justin A. Lemkul <[email protected]> wrote: > > > Aswathy wrote: > > >> >> On Wed, Aug 4, 2010 at 4:31 PM, Justin A. Lemkul <[email protected]<mailto: >> [email protected]>> wrote: >> >> >> >> Aswathy wrote: >> >> Dear Gromacs users, >> >> I am doing SMD of a ligand pathway, and then want ot do the PMF >> analysis. Initially I pulled the ligand from extra to >> intracellular side of the protein. The pull code used are given >> below. >> >> pull = umbrella >> pull_geometry = distance >> pull_dim = N N Y >> pull_start = yes >> pull_nstxout = 10 >> pull_nstfout = 10 >> pull_ngroups = 1 >> pull_group0 = r_57 >> pull_group1 = r_C1 >> pull_rate1 = 0.005 >> pull_k1 = 1000 >> >> here group0 is one residue at the extracellular region and r_C1 >> is the side chain Carbon atom of the ligand. >> >> My question is , the total length of the channel is almost 40 >> Angstrom and as per my knowledge, when we did the pulling the >> pullx file will give the coordinate of the ligand through the >> channel. >> >> >> Not quite. Look at the data labels in the .xvg file. The pullx >> file contains the coordinates (in all of the pull directions) for >> the reference group, and then the distance between the reference and >> the pull group along all pull axes. >> >> I am still confused. I have measured the distance between the reference >> group(residue outside) to the other end of the channel. that is around >> 40Angstrom. if so, 1dz should give around 40 Angstrom? Because once the >> pulling completed, the distance between group0 and group1 , should be equal >> to the length of the channel. >> >> > I guess I still don't understand your setup. Are you pulling a ligand > through a a channel and then beyond the reference group, out into some > solvent? Or are you just pulling the length of the channel, such that the > ligand never exits the channel. > > If you're pulling through the entire channel and then out into the solvent, > the sign of dZ is going to change. It might help if you post the first few > output lines of pullx.xvg (not the headers and stuff, the actual data), as > well as the last few. That way I can understand exactly what you're dealing > with. > > > Sorry that i am repeating the same query, i think I am still preconceived >> about this. Otherwise could you please suggest some good tutorial for the >> same . I will read that. >> >> > There is a pulling tutorial on the Gromacs website, but nothing that deals > with what you're doing. Tutorials are designed to generally guide the user > through a larger procedure, not explain every small piece of analysis. > > -Justin > > >> >> >> Even though ligand reaches the opposite end of the channel, in >> pullx file I am getting around 19 Angstrom in total. >> >> Again I calculate the g_dist of the ligand and the center of the >> channel, it shows around 40 Ang in total . Please find the links >> provided >> >> >> You're measuring two different things. The pullx distance is given >> relative to your pull_group0, which you said is a residue on one >> side of the channel. Then you're using g_dist to measure to the >> center of the channel. >> >> Am I misunderstanding anything about the pullx file. >> >> Could you please suggest me where thing get wrong? >> >> >> http://docs.google.com/fileview?id=0B1PyTWWGrqt6N2IyNjNhM2UtMzRiZC00MTJmLTg5ODItODJlMzQ5YTM3OGMy&hl=en >> < >> http://docs.google.com/fileview?id=0B1PyTWWGrqt6N2IyNjNhM2UtMzRiZC00MTJmLTg5ODItODJlMzQ5YTM3OGMy&hl=en >> > >> < >> http://docs.google.com/fileview?id=0B1PyTWWGrqt6N2IyNjNhM2UtMzRiZC00MTJmLTg5ODItODJlMzQ5YTM3OGMy&hl=en >> < >> http://docs.google.com/fileview?id=0B1PyTWWGrqt6N2IyNjNhM2UtMzRiZC00MTJmLTg5ODItODJlMzQ5YTM3OGMy&hl=en >> >> >> >> >> http://docs.google.com/fileview?id=0B1PyTWWGrqt6ZWRlZGJkOTgtMGEwYi00MzE0LThiZTEtM2JjNmJkMWU5NDYy&hl=en >> < >> http://docs.google.com/fileview?id=0B1PyTWWGrqt6ZWRlZGJkOTgtMGEwYi00MzE0LThiZTEtM2JjNmJkMWU5NDYy&hl=en >> > >> < >> http://docs.google.com/fileview?id=0B1PyTWWGrqt6ZWRlZGJkOTgtMGEwYi00MzE0LThiZTEtM2JjNmJkMWU5NDYy&hl=en >> < >> http://docs.google.com/fileview?id=0B1PyTWWGrqt6ZWRlZGJkOTgtMGEwYi00MzE0LThiZTEtM2JjNmJkMWU5NDYy&hl=en >> >> >> >> >> For some reason these documents are inaccessible. It is probably >> better to use a site like photobucket and post actual images. >> Google is great, but not everyone has an account and I've also been >> told that their usage agreement is troubling, in that anything you >> upload to Google Docs becomes property of Google. Not something >> I've looked into, but I don't ever post my research data there. >> >> >> -Justin >> >> >> Thank you, >> -- -Aswathy >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list [email protected] >> <mailto:[email protected]> >> >> 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 [email protected] >> <mailto:[email protected]>. >> >> 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Aswathy
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