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

From: Jan-Philip Gehrcke <>
Date: Fri, 09 Mar 2012 15:28:38 +0100

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.


On 02/20/2012 08:17 PM, Jan-Philip Gehrcke wrote:
> On 16.02.2012 15:33, David A Case wrote:
>> On Fri, Jan 27, 2012, Jan-Philip Gehrcke wrote:
>>> We're using Amber 11 (including all bugfixes up to last week) and
>>> observed a compiler-dependent error while parsing a DISANG file in
>>> sander. For ICC 12.1, things work properly, while for GCC 4.6.2, sander
>>> crashes. Details below.
>> Just a short, not-so-helpful note: the test case runs fine for me with
>> gcc
>> 4.6.1 on Mac OSX, 10.6.8.
>>> Result on Amber 11 compiled with GCC 4.6.2 on CentOS 5.7
>>> ========================================================
>>> Sander crashes "immediately".. presumably while parsing the `rest` file.
>>> min2.out:
>>>> Error: Invalid atom or grouping specified in restraint.
>>>> restraint = "torsion [:70.C1, :70.O5, :70.C5, :70.C4]"
>> A quibble: sander stops with an error message, which is somewhat
>> different
>> than a "crash".
> Right you are :-)
>> Have you tried removing the spaces after the commas above?
>> Can you tell if all "natural language" restraints fail, or just
>> certain ones?
> I will work on these things.
>> We'll continue to try (using virtual machines) to reproduce the error.
>> If anyone has easy access to CentOS 5.7 (or other Linux with gcc
>> 4.6.2) they
>> might try it. The original test case is attached.
> I should clarify and add that CentOS 5.7 originally comes with GCC 4.1.2
> (which makes certain test cases fail and is not recommended for Amber,
> right?). Therefore, I had built the GCC 4.6.2 (which I had used to build
> Amber(tools)) from source using GCC 4.1.2.
> Now, it would definitely be good to reproduce this problem on a system
> that natively comes with GCC 4.6.2, e.g. Fedora 16. I'll try to do so.
>> ...thx...dac
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Received on Fri Mar 09 2012 - 06:30:02 PST
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