Diana Rodriguez Ortiz wrote:
Hi Mr. Spoel,
I am working with a small protein (50 aminoacids) that has a metal atom
near its center. Where can I find the
parameters to be able to run a molecular dynamics of this protein? In this
one, the metal is tied to 4 sulfurs I will
run it with gromacs. Can you help me?
This is not simple, you will have to search the literature and/or
perform quantum calculations to obtain charges. You do not give much
details though. What metal? Is it tetrahedrally coordinated, i.e. is the
metal shielded from the environment completely? In that case you can
make chemical bonds using the specbond method.
Please continue this discussion on the gromacs mailing list.
Cordiially,
Diana Rodriguez
Intern at RPI
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Antes ahora y siempre COLEGIO
University of Puerto Rico at Mayaguez
http://www.uprm.edu
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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