Please keep all Gromacs-related correspondence on the gmx-users list. I am not
a private tutor or help service, and you stand a much better chance of getting
an answer by contacting the community.
I have never worked with a system like yours, so I don't know why you'd assume I
have such a protocol. In general, you should principally be concerned with
deriving proper parameters for your copper ion and quinone:
http://www.gromacs.org/Documentation/How-tos/Parameterization
Please realize that parameterization is a very advanced topic (especially note
the "Exotic Species" heading in the above page).
I have no idea what you mean by "the heteroatoms are getting converted to atoms"
- is there some issue with PDB nomenclature (HETATM/ATOM)? If so, there is no
problem.
-Justin
charanya wrote:
Dear Mr. Justin A. Lemkul,
I am working on copper dependent amine oxidases which have quinone and copper
cofactors. These are essential for the proper functioning of the enzyme.When I tried
to minimize the complex, the heteroatoms are getting converted to atoms. I request you
to kindly provide me with a protocol as to how to minimize these kind of proteins.
Thank you for your time and consideration.
Regards,
Charanya Muralidharan
Dept of Biochemistry, cell biology & Bioinformatics
Sankara Nethralaya
18 College Road
Chennai . 600 006
Phone: 044-28271616 Fax: 044-28254180
Please visit our web site: www.supportsankaranethralaya.org
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========================================
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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