[gmx-users] Help reg. EM
varma1 at uiuc.edu
Wed Jun 9 22:33:19 CEST 2004
I have been trying to energy minimize the structure of a protein complex
but it has "exploded" in all the attempts that I have made so far.
THE FINAL GOAL: To create a homology model of a protein complex that has a
known x-ray structure. In my case, the protein complex consists of 5 small
proteins, each having close to a 100 residues. The x-ray structure clearly
reveals the relative orientations of each segment.
WHAT WAS DONE: I independently created homology models of each of these
segments. I placed these segments in their proper relative orientations.
One can easily imagine that this would generate some steric violations. In
order to get rid of these steric violations, I thought that I could use an
I tried using both steepest descent and CG algorithms, tried a range of
step sizes (0.01-0.0001nm), tried several different force-fields (gromos96
united atom, OPLS/gromacs all atom, gromos vacuum), tried using backbone
freeze groups or backbone harmonic restraints (which is not advisable!),
but in all cases, I find the same "strange" result. After just 1 step, all
the segments are thrown apart. What I mean is, before EM, the segments were
in close contact with each other. And after 1 step of EM, they are about
15-20A away from each other.
What I fail to understand is, how could such a thing happen when the
maximum displacement allowed by the algorithm in one step is bounded by the
step size? Could this be a numerical issue?
Secondly and obviously: What can I do to fix this problem?
More information about the gromacs.org_gmx-users