Subject: parameters for 5'-phosphate GUA

From: Linjing Yang <[email-masked]>
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