RE: amber-developers: Serious problems with Antechamber runs due to faulty Mopac in AmberTools?

From: Scott Brozell <>
Date: Fri, 11 Jul 2008 15:20:13 -0700 (PDT)


I also verify that x86_64 with both g77 and gfortran has the mopac problem:
Linux 2.6.18-92.el5 #1 SMP Tue Apr 29 13:16:15 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux
Red Hat Enterprise Linux Server release 5.2 (Tikanga)
g77: gcc version 3.4.6 20060404 (Red Hat 3.4.6-4)
gfortran: gcc version 4.1.2 20071124 (Red Hat 4.1.2-42)

I tried reverting to revision 1.1 of block.f eliminating the only recent
mopac source changes; this had no effect.
-O0 -g also had no effect.
One avenue is -fbounds-check which yields a quick:
Subscript out of range on file line 43, procedure jcarin.f/jcarin.
Attempt to access the 4-th element of variable coord[subscript-1-of-2].
And now Im punting since Ross is the mopac expert ;-)

I agree that we should be very very careful when updating .save outputs.
I agree that we should be testing mopac.
But Im distancing myself from the sky is falling world of Ross since
I have seen similar partial charge differences have little affect
on docking results.
In addition, broken stuff has great pedagogical potential.

For the record these platform do not have the mopac problem:

Darwin 7.9.0 Darwin Kernel Version 7.9.0: Wed Mar 30 20:11:17 PST 2005; root:xnu/xnu-517.12.7.obj~1/RELEASE_PPC Power Macintosh powerpc
gcc version 3.3 20030304 (Apple Computer, Inc. build 1495)
g77: gcc version 3.4.0 20040107 (experimental)

Linux piv-login1 #12 SMP Sun Feb 10 17:08:11 EST 2008 i686 i686 i386 GNU/Linux
Red Hat Enterprise Linux AS release 3 (Taroon Update 6)
gcc version 3.2.3 20030502 (Red Hat Linux 3.2.3-53)

good luck,

On Fri, 11 Jul 2008, Ross Walker wrote:

> Okay here is a summary of the mopac problems on my machine
> RHEL4, Intel Pentium-D x86_64
> g77 (gcc version 3.4.6 20060404 (Red Hat 3.4.6-9)) - Suffers from the
> problems discussed.
> gfortran (gcc version 4.1.2 20070626 (Red Hat 4.1.2-14)) - Also suffers from
> the same problem.
> g95 (gcc version 4.0.3 (g95 0.92!)) - Gives a segfault very early on.
> ifort (Version 10.1 Build 20070913 Package ID: l_fc_p_10.1.008) - Works
> correctly (with extra output issues)
> Using -O0 with g77 or gfortran does not fix things.
> Trying to print the values of TIMITR, TIMES and DEBUG that control the
> printing of all the extra info that appears in the ifort output fixes the
> problem implying that there is some memory issue somewhere that is
> scrambling things.
> I will see if I can track down where the problems are - this is all due to
> numerous memory stomping issues and missing variable initializations - mopac
> 6.0 is full these :-(.
Received on Sun Jul 13 2008 - 06:07:54 PDT
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