Re: AMBER: ambpdb TER problems

From: Sam <>
Date: Tue, 27 Dec 2005 17:23:39 +0100

David A. Case wrote:

>Can you post the "protein.pdb" file? Do you have the same TER card problem
>if you don't solvate things? [That would allow us to create a much smaller
>test case....]

Indeed, it turns out that the ambpdb-misplacement of TER card
only happens after I have solvated the structure. Curious.. This
is independent of whether or not I have added K+ ions to the
structure (or in which order I do these two steps).

An xleap "check" of the solvated structure does not reveal any
"close contact" warnings with respect to water molecules with
either the CSER or DA5 residues.

I have temporarily posted the following files for xleap manipulation
of protein.pdb. Please note that the residue modification libraries
are unpublished works-in-progress and are not yet intended to be
used as "optimized" parameterizations.

Thanks for your help --

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Received on Wed Jan 04 2006 - 18:16:59 PST
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