AMBER Archive (2006)

Subject: Re: AMBER: xleap problems

From: David A. Case (case_at_scripps.edu)
Date: Mon Dec 04 2006 - 10:26:20 CST

On Mon, Dec 04, 2006, anna.schrey_at_gmx.de wrote:
> Dear amber community,
>
> I am using new parameterised residues, one of which causing problems. When I try to read an pdb file containing this residue which has been generated using ambpdb, into xleap, xleap crashes and I get error messages as follows:
>
> fenix 54% !FATAL ERROR----------------------------------------
> !FATAL: In file [chirality.c], line 121
> !FATAL: Message: Atom CT1 is not in the first list
> !
> !ABORTING.
>
> This does not happen if I read in a pdb file which contains the new residue only.
>

This problem is usually caused by bad connectivity in your new residue. Make
sure that the connect atoms are set properly. (Use the "desc" command in leap
to see what these are).

>From the error message, it looks like you are probably running Amber 8 but
without bugfix.15 applied. You will get a lot more information about the
problem if you apply that bugfix (and the others as well).

...dac
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