AMBER Archive (2006)

Subject: AMBER: Modifying a Force Field

From: Seth Lilavivat (sethl_at_gatech.edu)
Date: Tue Nov 28 2006 - 09:27:08 CST

Dear Amber Community,

I am trying to add my own force field parameters to the AMBER.dat file in the
/dat directory of the program PDB2PQR. Here is an excerpt of what is contained
in the file:

DA P 1.165900 2.1000 0.2000
DA O1P -0.776100 1.6612 0.2100
DA O2P -0.776100 1.6612 0.2100
DA O5' -0.495400 1.6837 0.1700
DA C5' -0.006900 1.9080 0.1094
DA H5'1 0.075400 1.3870 0.0157
DA H5'2 0.075400 1.3870 0.0157
DA C4' 0.162900 1.9080 0.1094
DA H4' 0.117600 1.3870 0.0157
DA O4' -0.369100 1.6837 0.1700
DA C1' 0.043100 1.9080 0.1094
DA H1' 0.183800 1.2870 0.0157

My question is - what information is contained in the right 3 columns, and how
would I add this information for my own molecule (where would I get it from or
how would I generate it)?

Thanks,
SETH
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