sonali dhindwal wrote:
Hello All
This question may sound trivial to many, but as i am new to this field,
please help.
I want to ask a question regarding my previous query of distortion of
protein strucutre after molecular dynamcs simulation.
Can you provide a link to your previous post, for reference?
I have noticed that after enegry minimisation using steepest decent
algorithm, using emtol of 1000 kJ mol^-1 nm^-1 .
So is it necessary to do enegry minimisation step before MD, because
this is my modeled protein, and i have already done energy minimisation
using different program and after that I have done refinement also.
Have you added solvent or anything else to the protein model? If so, then the
answer is yes. Solvation with a regularly-ordered lattice of solvent molecules
can (and often does) lead to bad clashes with your protein structure, thus
necessitating further minimization.
There are plenty of reasons why a protein structure might be unstable, most of
them related to .mdp file settings, but you haven't posted those so there's no
way to know if you're doing things correctly.
-Justin
Thanks and regards
^
--
Sonali Dhindwal
--
========================================
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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