Miguel Quiliano Meza wrote:
Dear Users.
I am a relative new user of GROMACS and I have some doubts:
I would like to perform a energy minimization (with water and iones) of
a crystal in orden to re-build the H-bonds responsible of the secundary
structure, to achieve this goal I want to restraint the movement of the
protein (aminoacids) and permit the movement of the H-bonds as a
product of add Hydrogens with pdb2gmx.
I think that this task could be define/establish in CONSTRAINS in
the ".mdp" file, I searched in the web and only find this:
First, understand that a "constraint" and a "restraint" are very different
concepts in Gromacs:
http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints
Thus, the "constraints" keyword is unrelated to what you're looking to do.
Simple energy minimization will seek to relax the structure, forming favorable
contacts and resolving large forces. Whether or not this bears any useful
information about the stability of secondary structure is debatable. Running
true MD is a better tool for that purpose, but EM should suffice to form any
hydrogen bonds that are reasonably close in space.
I don't think it will be meaningful at all to restrain part of the protein and
hope that hydrogen bonds in the backbone re-orient. You'd essentially be fixing
the side chain positions, which will not allow for much re-organization, not
that I'd expect to see major changes during EM, anyway.
-Justin
Bonds
constraints:
*none*
No constraints except for those defined explicitly in the
topology, i.e. bonds are represented by a harmonic (or other)
potential or a Morse potential (depending on the setting of
*morse*) and angles by a harmonic (or other) potential.
*hbonds*
Convert the bonds with H-atoms to constraints.
*all-bonds*
Convert all bonds to constraints.
*h-angles*
Convert all bonds and additionally the angles that involve
H-atoms to bond-constraints.
*all-angles*
Convert all bonds and angles to bond-constraints.
What option shoud I use for my objective? My objetive, is it possible to
do? I would be very grateful if someone can help me with some ideas or
advices.
thanks in advance
Miguel
--
========================================
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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