Hassan Shallal wrote:
Thanks a lot Justin for the valuable feedback about generating different velocities a few days ago...
I would like to discuss some analysis questions with the gromacs users, I tried to find solutions to the following points in the literature and/or the mailing list, unfortunately, couldn't find any..
1- Traget: measuring the energetics of interaction (Coulomb and LJ) between certain loops within the protein structure using g_energy or g_enemate
Plan: making index files with those specific loops and use the .ndx file to
introduce these groups to the g_energy using the -n option as mentioned in one
of the threads in the mailing
list(http://lists.gromacs.org/pipermail/gmx-users/2008-December/038588.html)
Problem: g_energy compiled from gormacs 4.5.2 version doesn't have an option
for index files!!
g_enemate has an option for groups.dat file, when I changed my loops.ndx to loops.dat and tried
to use it with g_enemate, g_enemate was not able to deal with it!!
Question: Is there anyway I can get the above measurment using gromacs
analytical tools?
Using special energy groups requires the use of energygrps in the .mdp file to
collect the proper energy terms during the simulation. If you did not do this,
you can re-run your simulation using mdrun -rerun in conjunction with a .tpr
file that contains the groups you want. Otherwise, neither g_energy no g_enemat
will produce anything like what you want; the decomposed energy terms simply do
not exist.
2- Traget: measuring time evolution of the size of a binding pocket along the
trajectory.
Approach: I was thinking that the volume of a a binding pocket between cerain
loops of the studied protein can be related to the number of water molecules
being able to occupy this pocket which by changing along the time trajectory
can give a quantitative (yet simplified) picture about the time evolution of
the volume of that pocket
Question: is there anyway to measure the size (volume) of a given binding
pocket using .ndx file of the surrounding loops and a specific analysis tool in
Gromacs?
No.
Question: If the answer to the above question is no. Would my approach of
measuring the number of the solvent molecules occupying this pocket make sense?
and if yes, how can I do this using Gromacs analytical tools?
Maybe. There is no standard Gromacs tool for doing this, however. There are
various other programs that may be able to handle such a task, like HOLE
(http://d2o.bioch.ox.ac.uk:38080/), cavity
(http://eels.kuicr.kyoto-u.ac.jp/~tnemoto/crystal/cavity/index.en.html), or
g_count (http://sbcb.bioch.ox.ac.uk/oliver/software/), but having never used the
first two extensively, I can't attest to their applicability. I used g_count
with version 4.0.7, but I don't know if it's compatible with the 4.5 series.
It may be worthwhile to look through the literature here. I'm sure there are
others who have done such analysis and other programs that I didn't list here.
-Justin
I would appreciate discussing the above questions and giving any hints or
answers
Regards
Hassan
--
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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