Justin A. Lemkul wrote:
For what it's worth, I've had this experience with some molecules
before with phosphatidic acid derivatives. It seems to only happen
during in vacuo EM. When in the presence of solvent or bound to a
protein it is less of an issue since the surrounding tends to
out-compete intramolecular interactions. The biggest problem is in
bilayers, where I've gotten around exploding molecules by setting
[exclusions] between the H and all phosphate O atoms. After solvation,
the problems tend to go away, since the solvent can satisfy the strong
electrostatic interactions in these parts of the molecule.
I should clarify that I remove any [exclusions] after doing EM, since solvated
systems seem to be stable enough to not need these artificial settings.
-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
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