Re: [AMBER] compiler-dependent error: "Invalid atom or grouping specified in restraint."

From: David A. Case <>
Date: Sun, 11 Mar 2012 13:54:23 -0400

On Fri, Mar 09, 2012, Jan-Philip Gehrcke wrote:

> I've set up a virtual machine running Fedora 16, which natively comes
> with GCC 4.6.2. There, I've build Amber 11 + AmberTools 1.5 with all
> bugfixes to date and was *not* able to reproduce the problem.
> I would think that the GCC 4.6.2 built via GCC 4.1.2 is just "as good"
> as the native GCC 4.6.2 of Fedora (whatever they build it with). So..
> the problem does not seem to be directly related to GCC 4.6.2.
> The occurrence of the problem also does not depend on spaces or brackets
> or these kinds of things: I've tried defining the torsional restraint in
> the natural language with different bracket types, with and without
> spaces/commas and with atom numbers instead of ambmasks. On the
> 'invalid' system, the error "Invalid atom or grouping specified in
> restraint." appeared in all of these cases.
> Hm.. is this still worth to further investigate? I am running out of ideas.

> >>> Result on Amber 11 compiled with GCC 4.6.2 on CentOS 5.7
> >>>> Error: Invalid atom or grouping specified in restraint.
> >>>> restraint = "torsion [:70.C1, :70.O5, :70.C5, :70.C4]"

Thanks for the information. As I understand it, this seems(!) to be related
to CentOS 5.7, or possibly to something peculiar to your particular
installation. I'm personally tied up with other commitments right now, but
someone may be able to reproduce the problem, then try to debug it. It sounds
like you may have a workaround for now (i.e. run on the Fedora machine, not
the CentOS one.)


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Received on Sun Mar 11 2012 - 11:00:02 PDT
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