[gmx-users] Problem in pullx file
Justin A. Lemkul
jalemkul at vt.edu
Thu Aug 5 14:14:17 CEST 2010
Aswathy wrote:
> 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
>
This looks exactly correct, although it appears you're dealing with some
periodic jumps across the box (hence +/- 5.4 nm). If the initial displacement
is roughly -0.7 nm and the final distance is -5.4 nm, then you've pulled 4.7 nm,
and if you subtract the fact that the reference group moved 0.7 nm (from 7.7 nm
to 8.4 nm), you pulled exactly 4.0 nm. I don't know how you came up with 1.9 nm
earlier.
-Justin
> Thanks,
> Aswathy
>
> On Thu, Aug 5, 2010 at 4:28 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> Aswathy wrote:
>
>
>
> On Wed, Aug 4, 2010 at 4:31 PM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> 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=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>>
>
> <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> <http://vt.edu> | (540)
> 231-9080
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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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 <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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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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