[gmx-users] Re: Query regarding Gromacs

[Justin A. Lemkul]

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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-- 
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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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