Josmar R. da Rocha wrote:
Dear Gromacs users
I set a 8 ns MD simulation aiming to get a view insight a hypothesized
open and closed state of a protein loop. Many crystallografic structures
have been solved but none of then shows the open state. Besides bfactor
for the loop region to be high, when analysing a partial result (at 2.5
ns) I could not see any intense conformational change (nor any such open
state). I noticed that there are two HB stabilizing the closed state.
1- Was the time I set too short?
Maybe; it is hard to say for sure.
2- How much time should set to make possible these interactions to break
to allow the open state conformation (I've seen in literature times
ranging from 2 to 120 ns to study loop movements).
Protein motions are difficult to predict. Some may oscillate very quickly
(within a few ns), others may be very slow (tens/hundreds of ns or more).
3- Since the time versus protein backbone RMSD plot shows the
equilibration of protein structure after some time is it reasonable to
imagine that after that it is not possible such loop movement to be
achieved?
Never say never :) Realize that simulations are random, so you may have to run
several different simulations, starting from different initial velocities, to
get better conformational/statistical sampling. Normal modes analysis may also
be appropriate for your system, depending on the degree of conformational
flexibility of your protein.
-Justin
I apologize If my questions sound naive but that's my first MD
simulation. I'd appreciate any help.
Josmar Rocha
------------------------------------------------------------------------
Novos endereços, o Yahoo! que você conhece. Crie um email novo
<http://br.rd.yahoo.com/mail/taglines/mail/*http://br.new.mail.yahoo.com/addresses>
com a sua cara @ymail.com ou @rocketmail.com.
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
http://www.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
--
========================================
Justin A. Lemkul
Graduate Research Assistant
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://www.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
