Re: [AMBER] AmberTools suppose program

From: David A Case <case.biomaps.rutgers.edu>
Date: Tue, 9 Dec 2014 21:56:18 -0500

On Tue, Dec 09, 2014, Yu Chen wrote:
>
> On OS X 10.6.8, I used macports gcc45. The compiling went without any
> problems. (make suppose). But when I try to run it with some pdb files
> (./suppose -fit ":15-18,106-109:C*,N*,O*,P" ./oldpdb/*.pdb or similar
> command), it just dies with "Segmentation fault".

I can reproduce this, but not quite understand how it has stopped working.
On the other hand, suppose.nab was last updated in 2000 (!), and somehow the
nab compiler has moved on....

As a workaround, please use the "suppose.nab" that is attached: compile as
before, put into your path, and give this a try. This bypasses an error
message, so be on the lookout for messages like this:

   superimpose: atom mismatch: ....

I'm cc-ing this to Tom Macke, who may have some insight here: Tom: see the
attached code at line 211-212, which is segfaulting. Looks like some
conflict between REF_MATRIX_T and MATRIX_T.)

Thanks for the report; it is clear that not many people are using suppose,
so be sure to report any other problems you have.

....dac



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Received on Tue Dec 09 2014 - 19:00:02 PST
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