parameters for 5'-phosphate GUA

From: Linjing Yang <yanglj_at_biomath.nyu.edu>
Date: Wed 14 Nov 2001 15:22:47 -0500

Hello,

I am wondering if anybody knows the AMBER parameters and atom charges for
the following DNA residue of 5'-terminal phosphate GUA:

        O1P H5' H4' O4' dG
         | | \ / \ /
H5T-O5T--P-O5'-C5'---C4' C1'
         | | \ / \
        O2P H5'' C3'--C2' H1'
                     / \ / \
                    O3' H3'H2' H2''
                    |

In addition, which atom type should O5T belongs to, OH or O2?

Thanks in advance.

Linjing
Received on Wed Nov 14 2001 - 12:22:47 PST