AMBER Archive (2002)

Subject: model molecules for getting charges of DNA

From: Jiyoung Heo (jyheo_at_wag.caltech.edu)
Date: Sat Jun 08 2002 - 19:20:10 CDT

Dear Amber developers,

I am wondering what was the model compound to get the charges for DNA
base. I assume that it could be 1-methylpyrimidine or 9-methylpurine.
Was it deoxyribonucleoside?
I am trying to get the charges for a non-standard base.
When I looked at your all_nuc94.in, the sugar and phosphate parts have
common charges except C1' and H1'. How did you re-distribute your
residual charge of base part after you got the charges from QM
calculation?

Jiyoung