Dear Dr. Lemkul, Thank you very much for your reply. Your reply is very helpful to me.The reason for not using other better-defined method is that I did not know much about such methods at the beginning. I took the computational work by leaning myself (following manuals and references). I really appreciate your valuable suggestion.
Best Regards, Rui On Sat, Feb 2, 2013 at 1:34 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Florida International University Department of Chemistry & Biochemistry University Park Campus, Dr. Xiaotang Wang Research Group Miami, Florida 33199 rzhan...@fiu.edu (305)301-7879 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
