I would just add to this a clarification that if you don't know the way
that the protein and DNA bind, combining the PDB files won't give you the
right initial structure for the complex. You'll need to use some other sort
of program to do that part. If you don't care about the initial structure,
and plan to use Amber simulations along with your NOE data to come up with
a model for the complex, then that's different.
On Tue, Nov 27, 2012 at 7:44 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Nov 27 2012 - 09:00:02 PST
