AMBER: Prepgen

From: A Box <>
Date: Thu, 15 Feb 2007 15:15:21 +1100


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

The files i used are attached.

mainchain.pro4 (changed the charge to +1 for file). (+1 charge) (neutral)

Any help is greatly appreciated.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to

Received on Sun Feb 18 2007 - 06:07:14 PST
Custom Search