AMBER Archive (2007)

Subject: AMBER: Prepgen

From: A Box (boxtwin2_at_gmail.com)
Date: Wed Feb 14 2007 - 22:15:21 CST

Hi

I am trying to create a modified DNA base for use in a simulation. I have
covalently attached a drug to the DNA base pair and calculated the charges
in gaussian03. I then converted the file to an ac format and the created a
machine file to exclude the terminal protons on the DNA. I run prepgen and
obtain a prepin file. When I open the file in xleap and check the molecules
charge it comes up with a -0.826140 (molecule calculated with neutral
charge in gaussian) or 0.174000 (calculated with +1 charge on molecule).

I thought prepgen enabled you to make new residues and add them to other
systems and maintain a integer charge (0 or +1) when the terminal atoms were
excluded).

The files i used are attached.

mainchain.pro4 (changed the charge to +1 for ba_dg4.com.6-31G_SP.ac file).
ba_dg4.com.6-31G_SP.ac (+1 charge)
ba_dg3.com.6-31G_SP.ac (neutral)

Any help is greatly appreciated.




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