Re: [AMBER] amber7 vs xleap on 64bit machine

From: Scott Brozell <sbrozell.rci.rutgers.edu>
Date: Wed, 8 Sep 2010 19:49:23 -0400

Hi,

On Wed, Sep 08, 2010 at 04:31:57PM -0400, case wrote:
> On Wed, Sep 08, 2010, Rossella Noschese wrote:
>
> > when I typed gfortran --version this was the output
> > GNU Fortran 95 (GCC 4.0.0 20050519 (Red Hat 4.0.0-8))
>
> I think you will have to upgrade the compiler. GCC version 4.0.0 was the very
> first of the series that supported gfortran. As the date shows, it is more
> than 5 years old, and there were many bugs in early versions of gfortran.
> Version 4.1.2 is probably the very earliest that you should consider, and even
> that will not work correctly on some parts of Amber (but I think is OK for
> AmberTools(?)). Going to version 4.4.x would be even more desirable.

Yes AmberTools 1.4 is successfully built by
gcc version 4.1.2 20071124 (Red Hat 4.1.2-42)
Red Hat Enterprise Linux Server release 5.2 (Tikanga)
Linux opt.edu 2.6.18-128.1.1.el5 #1 SMP Mon Jan 26 13:58:24 EST 2009 x86_64 x86_64 x86_64 GNU/Linux

And the tests have only these minor diffs:

./antechamber/chemokine/1b2t.ac.dif
586c586
< ATOM 584 CZ ARG 37 7.93 -8.28 -14.37 0. CM 
---
> ATOM    584  CZ  ARG    37       7.93  -8.28 -14.37  0.        CA
706c706
< ATOM    704  CZ  ARG    44     -10.99   6.16   4.63  0.        CM
---
> ATOM    704  CZ  ARG    44     -10.99   6.16   4.63  0.        CA
765c765
< ATOM    763  CZ  ARG    47      -4.90   0.51   4.99  0.        CM
---
> ATOM    763  CZ  ARG    47      -4.90   0.51   4.99  0.        CA
1095c1095
< ATOM   1093  CZ  ARG    67     -12.58   0.95 -18.49  0.        CM
---
> ATOM   1093  CZ  ARG    67     -12.58   0.95 -18.49  0.        CA
1199c1199
< ATOM   1197  CZ  ARG    74     -14.14  16.11 -21.51  0.        CM
---
> ATOM   1197  CZ  ARG    74     -14.14  16.11 -21.51  0.        CA
./sqm/ch3f/ch3f.pm3.go.out.dif
40c40
<   QMMM:     5        5      F       -0.6079    1.0420   -0.4558
>   QMMM:     5        5      F       -0.5971    1.0439   -0.4655
### Maximum absolute error in matching lines = 1.08e-02 at line 40 field 5
./antechamber/chemokine/1b2t.ac.dif
586c586
< ATOM    584  CZ  ARG    37       7.93  -8.28 -14.37  0.        CM
---
> ATOM    584  CZ  ARG    37       7.93  -8.28 -14.37  0.        CA
706c706
< ATOM    704  CZ  ARG    44     -10.99   6.16   4.63  0.        CM
---
> ATOM    704  CZ  ARG    44     -10.99   6.16   4.63  0.        CA
765c765
< ATOM    763  CZ  ARG    47      -4.90   0.51   4.99  0.        CM
---
> ATOM    763  CZ  ARG    47      -4.90   0.51   4.99  0.        CA
1095c1095
< ATOM   1093  CZ  ARG    67     -12.58   0.95 -18.49  0.        CM
---
> ATOM   1093  CZ  ARG    67     -12.58   0.95 -18.49  0.        CA
1199c1199
< ATOM   1197  CZ  ARG    74     -14.14  16.11 -21.51  0.        CM
---
> ATOM   1197  CZ  ARG    74     -14.14  16.11 -21.51  0.        CA
./sqm/ch3f/ch3f.pm3.go.out.dif
40c40
<   QMMM:     5        5      F       -0.6079    1.0420   -0.4558
>   QMMM:     5        5      F       -0.5971    1.0439   -0.4655
### Maximum absolute error in matching lines = 1.08e-02 at line 40 field 5
./antechamber/chemokine/1b2t.ac.dif
586c586
< ATOM    584  CZ  ARG    37       7.93  -8.28 -14.37  0.        CM
---
> ATOM    584  CZ  ARG    37       7.93  -8.28 -14.37  0.        CA
706c706
< ATOM    704  CZ  ARG    44     -10.99   6.16   4.63  0.        CM
---
> ATOM    704  CZ  ARG    44     -10.99   6.16   4.63  0.        CA
765c765
< ATOM    763  CZ  ARG    47      -4.90   0.51   4.99  0.        CM
---
> ATOM    763  CZ  ARG    47      -4.90   0.51   4.99  0.        CA
1095c1095
< ATOM   1093  CZ  ARG    67     -12.58   0.95 -18.49  0.        CM
---
> ATOM   1093  CZ  ARG    67     -12.58   0.95 -18.49  0.        CA
1199c1199
< ATOM   1197  CZ  ARG    74     -14.14  16.11 -21.51  0.        CM
---
> ATOM   1197  CZ  ARG    74     -14.14  16.11 -21.51  0.        CA
./sqm/ch3f/ch3f.pm3.go.out.dif
40c40
<   QMMM:     5        5      F       -0.6079    1.0420   -0.4558
>   QMMM:     5        5      F       -0.5971    1.0439   -0.4655
### Maximum absolute error in matching lines = 1.08e-02 at line 40 field 5
### Maximum relative error in matching lines = 1.81e-02 at line 40 field 5
scott
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Received on Wed Sep 08 2010 - 17:00:03 PDT
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