GB in amber6

From: Prabal Maiti <>
Date: Thu 15 Aug 2002 17:26:22 -0700 (PDT)

I am trying to use Generalized Born model for a system of DNA/polymer
complex. For the polymer I have generated the FF using antechamber program
of AMBER7. I have built the DNA/polymer complex using xleap in
When I try to run a GB minimiztion in amber6 (using gbparm =
2) it exits saying
>Using modified Bondi radii and Tinker screening parameters
>Unable to find bonded partner for atom 5182

5182 happens to be of type hn.

However, with gbparm = 1 it runs fine.

Any suggestions?


Prabal K Maiti                   
Beckman Institute (139-74)             
California Institute of Technology         Tel:626-395-8151 (O)
400 South Wilson Avenue                       :626-744-1363 (H)                    
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Received on Thu Aug 15 2002 - 17:26:22 PDT
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