On Tue, Nov 27, 2012, ????????? wrote:
>
> Currently, I am using AMBER to solve one protein-DNA complex. I
> have got the protein structure in complex form by solution NMR,
> and the DNA has crystal structure. Inter molecular NOE can be used
> to calculate the complex structure. As there is no tutorial about
> simulation of protein-DNA complex, I wonder how to perform MD for
> the system of two separated structures with experimental data?
Well, there are tutorials about proteins, and tutorials about DNA. Combining
them non-covalently is straightforward: just put one after the other into a
PDB-format file, and put TER cards between separate chains.
....good luck...dac
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Received on Tue Nov 27 2012 - 05:00:02 PST
