[AMBER] question about possible failures during Amber10 and AmberTools1.2

From: Gordon Freeman <gfreeman.wisc.edu>
Date: Fri, 29 Jul 2011 08:58:02 -0500

Quick question,

After waging war against gcc4.1.2 (thanks to the listserve archive I
discovered that there have been problems similar to mine reported in
the past about 4.1.2) I compiled Amber10 with gcc version 4.4.0 and
had considerably more luck. The tests that "possibly" failed are
below. Previous advice on the listserve was to not worry about
rounding errors in the very small decimal places and to copy errors of
greater magnitude here for comments.

If anyone can take a quick look and let me know if the tests reported
in TEST_FAILURES.diff are meaningful, I would be very appreciative!
FYI I will be using Amber10 for MD simulations of protein with both
implicit and explicit solvent in conjunction with PLUMED (hence using
Amber10 rather than Amber11).

-The first failure (AMBERHOME/test/tip5p) seems innocuous as the test
output file is identical to .save for the fact that rms fluctuations
were not calculated for EKCMT, VIRIAL, VOLUME, and Density in the test
output file (not sure why but this problem does seem to have come up
in any other test cases).
-The failure occuring for AMBERHOME/test/jar seems maybe a bit more
nefarious (markedly different output in the line that differed)? But I
do not know much about it so any comments would be helpful.
-Otherwise all failures occur in the last decimal place which leads me
to believe that I should not worry but assumptions like that can lead
to trouble...

Thanks a million!
-Gordo


For Amber10:

possible FAILURE: check mdout.tip5p.dif
AMBERHOME/test/tip5p
180,181d179
< EKCMT = 0.2952 VIRIAL = 9.6699 VOLUME
= 0.0001
< Density
= 0.
---------------------------------------
possible FAILURE: check gcg.dip.o.dif
AMBERHOME/test/rdc
352c352
< 196 H5'1 DA 7 0.14 0.62 0.96 
---
 >       196 H5'1 DA     7      0.14      0.63      0.96
377c377
<       512 H5'1 DA    17      0.13      0.62      0.98
---
 >       512 H5'1 DA    17      0.13      0.63      0.98
---------------------------------------
possible FAILURE:  check mdout.jar.dif
AMBERHOME/test/jar
87c87
< R1 = -85.000 R2 =  15.000 R3 =  15.000 R4 = 115.000 RK2 =5000.000  
RK3 = 5000.000
---
 > R1 =   0. R2 =  15.000 R3 =  15.000 R4 = 115.000 RK2 =5000.000 RK3  
= 5000.000
---------------------------------------
possible FAILURE:  check first.pdb.dif
AMBERHOME/test/ambpdb_first_protein
2147c2147
< HETATM 2145  X   BMH G  62      29.312  38.819  37.740  0.  0.   62 N
---
 > HETATM 2145  X   BMH G  62      29.313  38.819  37.740  0.  0.   62 N
---------------------------------------
possible FAILURE:  check first.pdb.dif
AMBERHOME/test/ambpdb_first_rna
2493c2493
< HETATM 2491  X   BMH G   8      23.812   6.343 -13.815  0.  0.    8 N
---
 > HETATM 2491  X   BMH G   8      23.813   6.343 -13.815  0.  0.    8 N
2588c2588
< HETATM 2586  X   BMH G  39      15.716  26.812 -17.572  0.  0.   39 N
---
 > HETATM 2586  X   BMH G  39      15.716  26.813 -17.572  0.  0.   39 N
2734c2734
< HETATM 2732  X   BMH G  88     -20.948  -1.812  -9.912  0.  0.   88 N
---
 > HETATM 2732  X   BMH G  88     -20.948  -1.813  -9.912  0.  0.   88 N
---------------------------------------
For AmberTools1.2:
---------------------------------------
possible FAILURE:  check tp.mol2.dif
AMBERHOME/test/antechamber/tp
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       
-0.113000
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        
0.017200
10c10
<       4 CE1        -0.6460    1.8630   -0.2340 ca        1 TP       
-0.137300
 >       4 CE1        -0.6460    1.8630   -0.2340 ca        1 TP       
-0.137100
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
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       
-0.256100
16c16
<      10 H29        -0.7870   -0.0430   -0.9380 ha        1 TP        
0.134900
 >      10 H29        -0.7870   -0.0430   -0.9380 ha        1 TP        
0.136300
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        
0.132100
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        
0.133200
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        
0.142600
### Maximum absolute error in matching lines = 1.50e-03 at line 17  
field 9
### Maximum relative error in matching lines = 2.99e-02 at line 9  
field 9
---------------------------------------
possible FAILURE:  check DGN.mol2.dif
AMBERHOME/test/antechamber/guanine_amber
9c9
<       3 C5'         0.7880    2.1110    1.6740 CT        1 DGN       
0.112500
 >       3 C5'         0.7880    2.1110    1.6740 CT        1 DGN       
0.114600
11c11
<       5 H5'2        0.3510    3.0020    1.2230 H1        1 DGN       
0.036100
 >       5 H5'2        0.3510    3.0020    1.2230 H1        1 DGN       
0.038400
13c13
<       7 H4'         0.3920    3.0300    3.5720 H1        1 DGN       
0.097700
 >       7 H4'         0.3920    3.0300    3.5720 H1        1 DGN       
0.094900
17c17
<      11 N9          2.5910   -0.6790    3.7030 N*        1 DGN      
-0.223000
 >      11 N9          2.5910   -0.6790    3.7030 N*        1 DGN      
-0.221000
18c18
<      12 C8          2.8130   -1.1800    2.4370 CK        1 DGN       
0.408000
 >      12 C8          2.8130   -1.1800    2.4370 CK        1 DGN       
0.404700
20c20
<      14 N7          2.8670   -2.4880    2.3830 NB        1 DGN      
-0.597800
 >      14 N7          2.8670   -2.4880    2.3830 NB        1 DGN      
-0.593800
23c23
<      17 O6          2.7450   -5.2750    3.7200 O         1 DGN      
-0.600500
 >      17 O6          2.7450   -5.2750    3.7200 O         1 DGN      
-0.602500
30c30
<      24 N3          2.2840   -1.7490    5.8480 NC        1 DGN      
-0.670000
 >      24 N3          2.2840   -1.7490    5.8480 NC        1 DGN      
-0.672800
31c31
<      25 C4          2.5030   -1.7890    4.5060 CB        1 DGN       
0.119500
 >      25 C4          2.5030   -1.7890    4.5060 CB        1 DGN       
0.117300
33c33
<      27 H3'         2.8820    3.5360    2.4530 H1        1 DGN       
0.075100
 >      27 H3'         2.8820    3.5360    2.4530 H1        1 DGN       
0.077600
34c34
<      28 C2'         3.4250    1.6990    3.4390 CT        1 DGN      
-0.145000
 >      28 C2'         3.4250    1.6990    3.4390 CT        1 DGN      
-0.148500
### Maximum absolute error in matching lines = 4.00e-03 at line 20  
field 9
### Maximum relative error in matching lines = 6.37e-02 at line 11  
field 9
---------------------------------------
Gordon Freeman
Research Assistant
Molecular Dynamics and Statistical Mechanics Research Group
University of Wisconsin-Madison
http://www.engr.wisc.edu/groups/mtsm/index.shtml
gfreeman.wisc.edu
617.960.6165
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Received on Fri Jul 29 2011 - 07:00:05 PDT
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