AMBER Archive (2006)

Subject: Re: AMBER: problems with saving self-built molecules parameters

From: David A. Case (case_at_scripps.edu)
Date: Mon Nov 20 2006 - 11:33:25 CST

On Mon, Nov 20, 2006, Rachel wrote:
>
> Could not find angle parameter: HD - HD - HD

Use the "desc" command in LEaP to examine your HD atoms, and see what they are
bonded to. It looks like you are getting bonds between molecules, which you
don't want.

A wild guess: be sure that your TER cards have a space following the "TER ":
prior to bugfix.19 this was required to have them properly recognized in some
circumstances (esp. when the residue number before and after the TER card was
the same). It is possible that you either don't have this bugfix installed,
or that there is some other spot in the code that should have been fixed as
wasn't.

...good luck....dac

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