On 9/13/12 5:50 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Ah okey. Thank you.
I will write them.
Hmm, but the protein is a crystal structure from pdb with a resolution of
1.2. I already added the hydrogen atoms to this structure and there I
already minimized them and made a md run. And there were no errors. And
now I only added the phosphate to the minimized structure. So I thought
that I only had to minimize the phosphate and the residue it bound on.
Or is there a mistake in my thought here?
If adding the phosphate resulted in a crash, then clearly that's the problem. I
don't understand why you would run EM on just the phosphate and keep the rest of
the protein structure frozen. Again, that potentially prevents clashes from
being resolved. I don't understand what value there is in only minimizing the
phosphate.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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