AMBER Archive (2008)

Subject: AMBER: antechamber test failure

From: john smith (johnsmithgr8_at_gmail.com)
Date: Tue Oct 14 2008 - 00:47:28 CDT

Hi All,

I am currently using Amber on my Intel Pentium IV with 1GB RAM with RedHat
Linux EL4.
I have compiled AmberaTools with gcc, and Amber serial version with intel
fortran compiler (ifort).
However, when i run the AmberTools test, i get many Possible FAILURE's for
antechamber.
The entries in TEST_FAILURES.diff are

 possible FAILURE: check ash.mol2.dif

/opt/amber10/test/antechamber/ash

8c8

< 2 CH3 2.0000 2.0900 0. c3 1 ACE -0.172000

> 2 CH3 2.0000 2.0900 0. c3 1 ACE -0.172600

17c17

< 11 CB 5.6610 4.2210 -1.2320 c3 2 ASH -0.154000

> 11 CB 5.6610 4.2210 -1.2320 c3 2 ASH -0.154900

21c21

< 15 OD1 7.9620 4.3130 -0.6200 o 2 ASH -0.573300

> 15 OD1 7.9620 4.3130 -0.6200 o 2 ASH -0.572800

### Maximum absolute error in matching lines = 9.00e-04 at line 17 field 9

### Maximum relative error in matching lines = 5.84e-03 at line 17 field 9

              ---------------------------------------

possible FAILURE: check sustiva.mol2.dif

/opt/amber10/test/antechamber/sustiva

7c7

< 1 C1 0.7280 1.4030 0.2550 ca 1 SUS -0.046500

> 1 C1 0.7280 1.4030 0.2550 ca 1 SUS -0.044800

9c9

< 3 C2 0.8030 0.0800 -0.1500 ca 1 SUS -0.174000

> 3 C2 0.8030 0.0800 -0.1500 ca 1 SUS -0.179300

10c10

< 4 C3 -0.2900 -0.9320 0.1580 c3 1 SUS 0.328900

> 4 C3 -0.2900 -0.9320 0.1580 c3 1 SUS 0.314400

11c11

< 5 C4 -1.6350 -0.3520 0.0320 c1 1 SUS -0.189100

> 5 C4 -1.6350 -0.3520 0.0320 c1 1 SUS -0.190900

12c12

< 6 C5 -2.7180 0.1230 -0.0620 c1 1 SUS 0.016000

> 6 C5 -2.7180 0.1230 -0.0620 c1 1 SUS 0.014300

13c13

< 7 C6 -4.0440 0.6950 -0.1770 cx 1 SUS -0.084700

> 7 C6 -4.0440 0.6950 -0.1770 cx 1 SUS -0.081000

14c14

< 8 H2 -4.7410 0.3350 0.5580 hc 1 SUS 0.107000

> 8 H2 -4.7410 0.3350 0.5580 hc 1 SUS 0.105500

15c15

< 9 C7 -4.6000 1.0130 -1.5410 cx 1 SUS -0.104600

> 9 C7 -4.6000 1.0130 -1.5410 cx 1 SUS -0.106500

18c18

< 12 C8 -4.2070 2.1230 -0.6290 cx 1 SUS -0.110500

> 12 C8 -4.2070 2.1230 -0.6290 cx 1 SUS -0.111600

20c20

< 14 H6 -3.3140 2.6760 -0.8580 hc 1 SUS 0.081600

> 14 H6 -3.3140 2.6760 -0.8580 hc 1 SUS 0.082600

25c25

< 19 O1 -0.2320 -2.0480 -0.7120 os 1 SUS -0.396600

> 19 O1 -0.2320 -2.0480 -0.7120 os 1 SUS -0.373000

26c26

< 20 C10 0.8930 -2.5380 -1.2450 c 1 SUS 0.851000

> 20 C10 0.8930 -2.5380 -1.2450 c 1 SUS 0.836600

27c27

< 21 O2 0.9220 -3.6240 -1.7130 o 1 SUS -0.571500

> 21 O2 0.9220 -3.6240 -1.7130 o 1 SUS -0.578100

28c28

< 22 N1 1.9640 -1.6960 -1.2420 n 1 SUS -0.485200

> 22 N1 1.9640 -1.6960 -1.2420 n 1 SUS -0.473000

29c29

< 23 H7 2.7760 -2.0540 -1.6920 hn 1 SUS 0.354300

> 23 H7 2.7760 -2.0540 -1.6920 hn 1 SUS 0.356500

30c30

< 24 C11 1.9190 -0.3690 -0.8360 ca 1 SUS 0.106200

> 24 C11 1.9190 -0.3690 -0.8360 ca 1 SUS 0.107400

33c33

< 27 C13 2.8920 1.8170 -0.7000 ca 1 SUS -0.068000

> 27 C13 2.8920 1.8170 -0.7000 ca 1 SUS -0.066400

35c35

< 29 C14 1.7720 2.2620 -0.0180 ca 1 SUS -0.021100

> 29 C14 1.7720 2.2620 -0.0180 ca 1 SUS -0.019900

36c36

< 30 Cl1 1.6780 3.9240 0.4950 cl 1 SUS -0.074800

> 30 Cl1 1.6780 3.9240 0.4950 cl 1 SUS -0.076400

### Maximum absolute error in matching lines = 2.36e-02 at line 25 field 9

### Maximum relative error in matching lines = 1.19e-01 at line 12 field 9

---------------------------------------

possible FAILURE: check fluorescein.mol2.dif

/opt/amber10/test/antechamber/fluorescein

7c7

< 1 C1 2.5990 2.5020 0.1700 ca 1 FLR -0.436200

> 1 C1 2.5990 2.5020 0.1700 ca 1 FLR -0.438300

8c8

< 2 C2 1.9170 3.7710 0.1310 ca 1 FLR 0.591300

> 2 C2 1.9170 3.7710 0.1310 ca 1 FLR 0.588100

9c9

< 3 C3 0.4600 3.6850 0.0600 ca 1 FLR -0.307200

> 3 C3 0.4600 3.6850 0.0600 ca 1 FLR -0.310800

11c11

< 5 C5 0.4940 1.2500 0.1120 ca 1 FLR -0.313500

> 5 C5 0.4940 1.2500 0.1120 ca 1 FLR -0.316400

12c12

< 6 C6 1.9140 1.3260 0.1530 ca 1 FLR 0.461500

> 6 C6 1.9140 1.3260 0.1530 ca 1 FLR 0.443900

13c13

< 7 C7 -0.1270 -0.0030 0.1350 cc 1 FLR 0.242000

> 7 C7 -0.1270 -0.0030 0.1350 cc 1 FLR 0.236600

14c14

< 8 C8 0.6580 -1.1570 0.2180 cd 1 FLR -0.330900

> 8 C8 0.6580 -1.1570 0.2180 cd 1 FLR -0.327100

15c15

< 9 C9 2.0750 -1.0350 0.2570 cd 1 FLR 0.370000

> 9 C9 2.0750 -1.0350 0.2570 cd 1 FLR 0.378300

16c16

< 10 O10 2.6430 0.1900 0.2110 os 1 FLR -0.461000

> 10 O10 2.6430 0.1900 0.2110 os 1 FLR -0.415500

17c17

< 11 C11 0.1510 -2.4930 0.2710 cd 1 FLR 0.018200

> 11 C11 0.1510 -2.4930 0.2710 cd 1 FLR 0.012900

18c18

< 12 C12 0.9550 -3.5690 0.3820 cc 1 FLR -0.319000

> 12 C12 0.9550 -3.5690 0.3820 cc 1 FLR -0.329400

19c19

< 13 C13 2.4100 -3.4500 0.4510 c 1 FLR 0.575100

> 13 C13 2.4100 -3.4500 0.4510 c 1 FLR 0.585300

20c20

< 14 C14 2.9140 -2.1010 0.3740 cc 1 FLR -0.361900

> 14 C14 2.9140 -2.1010 0.3740 cc 1 FLR -0.391500

21c21

< 15 O15 2.5020 4.8520 0.1610 o 1 FLR -0.736500

> 15 O15 2.5020 4.8520 0.1610 o 1 FLR -0.746200

22c22

< 16 O16 3.1370 -4.4350 0.5740 o 1 FLR -0.712300

> 16 O16 3.1370 -4.4350 0.5740 o 1 FLR -0.706000

23c23

< 17 C17 -2.2520 -0.2510 -2.1800 c 1 FLR 0.892900

> 17 C17 -2.2520 -0.2510 -2.1800 c 1 FLR 0.903000

24c24

< 18 O18 -3.2360 -0.3500 -2.9170 o 1 FLR -0.830900

> 18 O18 -3.2360 -0.3500 -2.9170 o 1 FLR -0.856100

25c25

< 19 O19 -1.0600 -0.1820 -2.4550 o 1 FLR -0.812600

> 19 O19 -1.0600 -0.1820 -2.4550 o 1 FLR -0.784100

26c26

< 20 C20 -2.0180 -0.0630 1.6790 ca 1 FLR -0.150000

> 20 C20 -2.0180 -0.0630 1.6790 ca 1 FLR -0.138500

27c27

< 21 C21 -1.6170 -0.0950 0.3400 ca 1 FLR -0.028300

> 21 C21 -1.6170 -0.0950 0.3400 ca 1 FLR -0.038800

28c28

< 22 C22 -2.5820 -0.2060 -0.6630 ca 1 FLR -0.084400

> 22 C22 -2.5820 -0.2060 -0.6630 ca 1 FLR -0.097100

29c29

< 23 C23 -3.9220 -0.2800 -0.2810 ca 1 FLR -0.122600

> 23 C23 -3.9220 -0.2800 -0.2810 ca 1 FLR -0.118000

30c30

< 24 C24 -4.3130 -0.2480 1.0430 ca 1 FLR -0.159300

> 24 C24 -4.3130 -0.2480 1.0430 ca 1 FLR -0.167600

31c31

< 25 C25 -3.3500 -0.1380 2.0350 ca 1 FLR -0.159500

> 25 C25 -3.3500 -0.1380 2.0350 ca 1 FLR -0.166300

32c32

< 26 H26 3.6730 2.4940 0.2160 ha 1 FLR 0.126200

> 26 H26 3.6730 2.4940 0.2160 ha 1 FLR 0.128300

34c34

< 28 H28 -1.2630 2.4880 -0.0150 ha 1 FLR 0.118600

> 28 H28 -1.2630 2.4880 -0.0150 ha 1 FLR 0.122900

35c35

< 29 H29 -0.9130 -2.6280 0.2120 ha 1 FLR 0.116900

> 29 H29 -0.9130 -2.6280 0.2120 ha 1 FLR 0.124300

37c37

< 31 H31 3.9760 -1.9440 0.4130 ha 1 FLR 0.133200

> 31 H31 3.9760 -1.9440 0.4130 ha 1 FLR 0.128300

38c38

< 32 H32 -1.2660 0.0220 2.4440 ha 1 FLR 0.131500

> 32 H32 -1.2660 0.0220 2.4440 ha 1 FLR 0.121900

39c39

< 33 H33 -4.6410 -0.3640 -1.0730 ha 1 FLR 0.145100

> 33 H33 -4.6410 -0.3640 -1.0730 ha 1 FLR 0.155700

40c40

< 34 H34 -5.3580 -0.3070 1.3030 ha 1 FLR 0.093000

> 34 H34 -5.3580 -0.3070 1.3030 ha 1 FLR 0.096400

41c41

< 35 H35 -3.6300 -0.1110 3.0750 ha 1 FLR 0.089100

> 35 H35 -3.6300 -0.1110 3.0750 ha 1 FLR 0.098500

### Maximum absolute error in matching lines = 4.55e-02 at line 16 field 9

### Maximum relative error in matching lines = 4.11e-01 at line 17 field 9

---------------------------------------

Please give me the suggestion how to solve this problem

Thanks in Advance.

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