Re: [AMBER-Developers] test request for ambertools and Snow Leopard 64 bits kernel

From: Ben Roberts <>
Date: Mon, 30 Nov 2009 13:59:24 -0500

Hi Volodomyr,

Volodymyr Babin wrote:
> Hi Ben,
> thank you for the work you've done. I am not the bondtype author,
> but enjoyed playing with it and hence the curiosity regarding the
> possible bug. Could you please 'cvs update -d' in src/antechamber,
> then 'make bondtype.orig' and try it instead of the 'bondtype'
> [just to rule out few more possibilities].

OK, I've given that a go, to no real avail. It still dies in the same
place. I haven't filled the bondtype.cpp up with debugging statements,
as I suppose it's better to focus our energies on bondtype.c at present.

I've attached the output file I got from the C++ version, though it
doesn't really tell me anything new.

> As far as I could understand the 'bond2' array gets malloc-ed and not
> initialized (at least some members do not get initialized); therefore
> those different values are to be expected (it is just garbage). OTOH,
> this is not necessarily an error.

I understand. So much for an obvious and easy solution...


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Received on Mon Nov 30 2009 - 11:30:02 PST
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