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 <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Aswathy wrote:
On Wed, Aug 4, 2010 at 4:31 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@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
========================================
-- gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto: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 the www
interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
<mailto: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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
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 the www
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
