On 2/2/13 9:30 AM, Rui Zhang wrote:
Dear all,
Could anyone help me on my previous questions? Please reply me... (I know
it might be a hard question, and I did all the works by learning myself.)
I was very frustrated that the professor who works as the
co-author didn't use GROMACS (and GROMOS53a6 force field), but he concerned
about whether the heme charge is defensible before the manuscript can be
submitted. It takes me two years to write this manuscript. I was about to
graduate in this spring but have no paper published yet. I hope you can
give me some clue so that I can get the manuscript at least submitted.
The best answer to the original question is that there probably is no definitive
answer. There are a variety of ways in which people derive parameters for
Gromos96 force fields, but most involve empirical fitting and transferability
between equivalent groups. Dealing with metals and such can be quite challenging.
No one on this list is likely to give you a "peer review before peer review," if
you will, based solely on incomplete information in an email, and it probably
would have been better to ask questions before spending 2 years working on this
system - what if it turns out you were wrong all along? Why not use a force
field that has a better-defined method for deriving partial charges?
In any case, Gromos96 53A6 does in fact have parameters for heme, though the
charges are quite different from what you have derived. That's not to say that
your model isn't superior. What you have to demonstrate is that your model
provides some insight that can be compared to known experimental behavior.
That's the task of any simulation model.
-Justin
On Fri, Feb 1, 2013 at 10:49 AM, Rui Zhang <rzhan...@fiu.edu> wrote:
Hello,
I want to derive the atomic partial charges for heme in chloroperoxidase,
since these parameters cannot be found in the GROMOS53a6 force field.
Chloroperoxidase is a cysteine-ligated heme protein (high spin) much like
P450. In my work, I want to study the interactions between the protein
residues of chloroperoxidase and its substrates. Thus, I used the QM
software ORCA to optimize the heme-thiolate structure (TPSS/def2-SPVD), and
then I used CHELPG method to derive the heme charges. Could anyone tell me
if the method I used is suitable for my purpose?
In addition, the charges I obtained for Fe (0.931877) and nitrogen
(-0.44572, -0.34427, -0.39467, and -0.39467) are largely consistent with
two reference. The reference are one in 1995 (Fe: 1.0, N: -0.4; Helms et
al. Thermodynamics of water mediating protein-ligand interactions in
cytochrome P450cam: a molecular dynamics study, Biophys. J. 69: 810-24) and
one in recent (Fe: 0.847, N: -0.37, -0.423, -0.504, and -0.528; Favia et
al. (2006) Three-dimensional model of the human aromatase enzyme and
density functional parameterization of the iron-containing protoporphyrin
IX for a molecular dynamics study of heme-cysteinato cytochromes, Proteins
62: 1073-84). I will greatly appreciate any comment and suggestions.
Best Regards,
Rui
--
========================================
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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