AMBER Archive (2009)

Subject: [AMBER] "bad atom type"

From: Akansha Saxena (
Date: Fri Jan 09 2009 - 11:15:11 CST


I am trying run GB simulations (igb=2, gbsa=1) and have
defined a new atomtype in my system. Running Sander gives me an error
for "bad atom type".
I checked the amber-user archive and found that this error occurs because the surface area calculations (LCPO model) are not able to find parameters for the new atomtype. The
suggested solution was to add a line in mdread.f
($AMBERHOME/src/sander) with the new parameters.

I was
wondering if modifying the mdread.f file was the only solution to this
problem or is there anything in the prmtop file which I can updat to
prevent this error.



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