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
regards
balaji
UOM
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Received on Thu Nov 12 2009 - 04:30:02 PST
