AMBER Archive (2009)

Subject: [AMBER] reg. GBA

From: balaji nagarajan (
Date: Thu Nov 12 2009 - 06:06:30 CST

Dear Amber !

I tried doing Generalized Born Approach model
for the DNA having 20 basepairs .

I have followed the tutorial given for Oxytocin peptide.

I have minimized the structure and when I tried to do the
equillibration i had the problem saying error message "Bad atom type Ip"

when searching in the archive i got that this is due to
the charged ion but i have only Sodium Na+ to neutralize

I have gone up to $Amberhome/src/sander/mdread.f
as mentioned earlier in the archive but i dont know how to edit
in the program file .,

or it is not advaisable to add Sodium for neutralizing the DNA

can any one sugesst me to do it


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