AMBER Archive (2009)
Subject: [AMBER] reg. GBA
From: balaji nagarajan (balaji_sethu_at_hotmail.com)
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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