AMBER Archive (2004)

Subject: Re: AMBER: GB and Atom Type

From: David A. Case (case_at_scripps.edu)
Date: Tue Jan 20 2004 - 17:03:52 CST

On Tue, Jan 20, 2004, Steve Seibold wrote:

> However, once I switched to the Generalized Born solvation , using the
> same protein topology file used in the distance dependent run in vacuo
> above, the simulation failed to run and gave the following message: "bad
> atom type: FE".

The "SA" part (gbsa=1) does not have parameters for all atom types. You
would need to either set gbsa=0, or to modify the code around line 665 of
mdread.f to accommodate an iron atom type.

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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