AMBER Archive (2002)

Subject: GB in amber6

From: Prabal Maiti (maiti_at_wag.caltech.edu)
Date: Thu Aug 15 2002 - 19:26:22 CDT

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
amber6.
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 

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Prabal K Maiti                             Email:maiti_at_wag.caltech.edu
Beckman Institute (139-74)                       pkmaiti_at_yahoo.com
California Institute of Technology         Tel:626-395-8151 (O)
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