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.
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=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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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