James Starlight wrote:
Justin,
31 марта 2012 г. 18:18 пользователь Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> написал:
Start by inspecting the initial configuration in the vicinity of
these atoms. Something is likely clashing here.
Yes, I've checked both of the proteins and found that the problem atoms
were situated exactly in the docked region of the both proteins. So It
seems that there are some clashes between atoms in the docked site. By
the way this site of the first protein ( Receptor) consist of 2 flexible
loops and the rigid helix from the second protein. ( fragment of
G-protein) Might the energy minimisation solve this problem generally ?
( e.g by means of CG minimisation to very low forces aplied on atoms).
Is there any possible ways to change conformation of the flexible loops
during minimisation\ equilibration phases without aplication of any
external forces?
Proper EM should resolve such clashes, but under normal circumstances that
should have happened already. You may have to do EM in vacuo before adding any
solvent to allow for proper resolution of clashes. I'm only guessing at this
point. I have asked twice for the output of your previous EM attempts, which
would give me a much better idea of where things stand. Since you haven't
answered those questions, I'll leave it up to you to try to resolve. Good luck.
-Justin
--
========================================
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/Support/Mailing_Lists/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/Support/Mailing_Lists
