On Wed, Jul 27, 2011, Peter Varnai wrote:
>
> isn't it risky to use the same atom type name (i.e., C4/C5) both in
> nucleic acids and proteins (see ildn modifications) in case of overlap
> when simulating protein-nucleic acid complexes?
For the standard Amber force fields, the C4 and C5 atom types are not used
in proteins, only in nucleic acids. But you are correct: if you wanted to
use run a protein-RNA simulation with both the ildn protein modifcations
and the OL chi torsions, you would have to do some work to avoid naming
conflicts.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jul 27 2011 - 07:30:04 PDT
