AMBER Archive (2009)

Subject: [AMBER] Amber 1.2 tools test suite failure?

From: Jim Parker (jim.parker_at_prismsciences.com)
Date: Sat Apr 11 2009 - 12:41:54 CDT

Hello,
  I am attempting to build AmberTools 1.2 and Amber 10 on an Ubuntu 8.10
(Intrepid Ibex) system.

Following the guide in the INSTALL file, I was able to compile
AmberTools without errors. But moving to the test suite, it failed at

test.ptraj: (from Makefile_at)

the test ptraj_rmsa/Run.rmsa script is written for 'csh'. In fact all
the scripts in test.ptraj are in csh format. (I was surprised there
were not more questions on the archives related to this)
I was able to convert them to bash style, to run on Ubuntu, which gets
me to the next series of tests.

test.antechamber.hasG77:

Ubuntu does not install with g77, it uses gfortran-4.3.2, and so this
section would be skipped
as these depend upon mopac. But I was curious about them, and attempted
to figure out how to make them run.

mopac (the version with AmberTools) requires the input file to be named
FOR005 and generates 3 output files FOR011, FOR012, and FOR016.
There is a script mopac.sh provided by AmberTools as a wrapper for calls
to mopac so that the user can pass arguments on the command line,
something that the native Fortran program it was written in did not
support. And again it was written in csh, so I modified for use with bash.

The problem is that the first test in antechamber/tp/Run.tp calls
antechamber which in turn calls mopac.sh to set the charges, but it does
not pass any parameters--no names of input or output files--even though
the script was written to allow that. So I remodified the script to
just cp the file mopac.in to FOR005 and then mopac executes writing all
to mopac.out.

The question I have is that although the test runs to completion, the
result is "possible FAILURE: check tp.mol2.diff"
Can anybody tell me if the these results are OK?

>cat tp.mol2.diff

7c7
< 1 CG -1.9590 0.1020 0.7950 ca 1 TP
-0.118900
> 1 CG -1.9590 0.1020 0.7950 ca 1 TP
-0.118600
8c8
< 2 CD1 -1.2490 0.6020 -0.3030 ca 1 TP
-0.113400
> 2 CD1 -1.2490 0.6020 -0.3030 ca 1 TP
-0.113600
9c9
< 3 CD2 -2.0710 0.8650 1.9630 ca 1 TP
0.016700
> 3 CD2 -2.0710 0.8650 1.9630 ca 1 TP
0.016300
11c11
< 5 C6 -1.4720 2.1290 2.0310 ca 1 TP
-0.145000
> 5 C6 -1.4720 2.1290 2.0310 ca 1 TP
-0.145200
13c13
< 7 HE2 -1.5580 2.7190 2.9310 ha 1 TP
0.130300
> 7 HE2 -1.5580 2.7190 2.9310 ha 1 TP
0.129700
14c14
< 8 S15 -2.7820 0.3650 3.0600 sh 1 TP
-0.254900
> 8 S15 -2.7820 0.3650 3.0600 sh 1 TP
-0.254300
17c17
< 11 H30 0.3730 2.0450 -0.7840 ha 1 TP
0.133600
> 11 H30 0.3730 2.0450 -0.7840 ha 1 TP
0.133400
18c18
< 12 H31 -0.0920 3.5780 0.7810 ha 1 TP
0.132700
> 12 H31 -0.0920 3.5780 0.7810 ha 1 TP
0.133100
19c19
< 13 H32 -2.3790 -0.9160 0.9010 ha 1 TP
0.142800
> 13 H32 -2.3790 -0.9160 0.9010 ha 1 TP
0.143000
### Maximum absolute error in matching lines = 6.00e-04 at line 13 field 9
### Maximum relative error in matching lines = 2.45e-02 at line 9 field 9

I think that it probably is, but I'd like someone to check before I
continue modifying the other tests.
Also, would there be any interest in posting my edits to the testsuite?

Cheers,
--Jim Parker
UTSA Physics

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