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Add some Amber to NWChem comparisions

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This commit is contained in:
Kurt Glaesmann 2009-11-03 18:10:52 +00:00
parent c28152a3de
commit 70d69d5e27
37 changed files with 17047 additions and 0 deletions
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QA/amber-tests/README Normal file
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The dotests.msub MOAB script runs a bunch of NWChem and Amber runs, you might have to
edit it to set the right path and account number. The resulting test.out.* file
should be empty when the job completes.
Each one of these subdirectories is a seperate test with its own README file.
big: amino acid sequence
big.shake: amino acid sequence, which shake enabled
ethane: single ethane molecule
ethane+: single ethane molecule with a +4 charge
small: ALA dimer
methanol: solvent only run (NWChem only)
Within each directory is a README file that describes what results you should get.
-------
Hints for generating your own amber tests:
First you need a PDB file of the molecule of interest (assume this is tiny.pdb)
Do this in an xterm
module purge
module load amber/10
./xleap &
Fix the PDB to match amber based upon these files:
${AMBERHOME}/dat/leap/lib/all_amino94.lib ("normal" amino acids)
${AMBERHOME}/dat/leap/lib/all_aminont94.lib (N terminating)
${AMBERHOME}/dat/leap/lib/all_aminoct94.lib (C terminating)
Until all atoms are correctly named when you type:
tiny = loadPdb tiny.pdb on the xleap command line
For example, I had to change CD to CD1 in ILE
You may have to "edit tiny" to set atom types, add bonds, set charges, etc. I
had to do that with ethane (there was nothing in the default libraries, because
it is not an amino acid).
To add bonds, you must be in "draw" mode
Once you think you are done, type this in the xleap command line:
check tiny
If all is well then save it as tiny2 (note this this is new name, since we 'fixed' things).
savePdb tiny tiny2.pdb
saveOff tiny tiny2.lib
saveAmberParm tiny tiny2.top tiny2.cor
-------
Hints for NWChem runs:
The atoms might need changed to match *.frg files for NWChem
This is why the pdb files might not be the same for amber and NWChem

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This is a series of amino acids, with SHAKE ON
NWChem input files:
big.nw - nwchem input deck
big.pdb - pdb file with geometry
THR_N.sgm - amber95 segment file: one in SVN does not match
amber input files:
big_am.in - amber input deck
big_am.top - amber topology file
big_am.cor - coordinates
NWChem output files:
big.seq
big.nam
VAL.mat
THR.mat
SER.mat
PHE.mat
MET.mat
LEU.mat
ILE.mat
GLU.mat
big.top
big_md.rst
big_md.cmd
big.bsg
ASP.mat
ASN.mat
ARG.mat
ALA.mat
big_energy.out
big.out
big_md.qrs
big_md.out
big.db
amber output files:
mdinfo
big_am.rst
big_am.out
results from *.out files:
4.266015438E+03 kJ/mol for NWChem single point (10.1960E+02 kcal/mol)
-1.29173E+03 kJ/mol for 300 steps NWChem (-2.0873E+02 kcal/mol)
-2.70772E+03 kJ/mol for 1500 steps NWChem (-6.4716E+02 kcal/mol)
-2.70992E+03 kJ/mol for 3000 steps NWChem (-6.4769E+02 kcal/mol)
9.4289E+02 kcal/mol for amber single point
-4.5606E+02 kcal/mol for amber 300 steps
-6.4034E+02 kcal/mol for amber 1500 steps
-6.4192E+02 kcal/mol for amber 3000 steps
Note that they match, but I had to limit NWChem's maximum step size to get this

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# This file matches the amber force field
# 07/31/09 13:21:28
4.600000
16 15 26 33 0 0 1 1
0.000000
1 N 0 0 0 1 1
N3 0.181200 0.000000
22H 0 0 0 1 1
H 0.193400 0.000000
33H 0 0 0 1 1
H 0.193400 0.000000
44H 0 0 0 1 1
H 0.193400 0.000000
5 CA 0 0 0 1 1
CT 0.003400 0.000000
6 HA 0 0 0 1 1
HP 0.108700 0.000000
7 CB 0 0 0 1 1
CT 0.451400 0.000000
8 HB 0 0 0 1 1
H1 -0.032300 0.000000
9 CG2 0 0 0 1 1
CT -0.255400 0.000000
102HG2 0 0 0 1 1
HC 0.062700 0.000000
113HG2 0 0 0 1 1
HC 0.062700 0.000000
124HG2 0 0 0 1 1
HC 0.062700 0.000000
13 OG1 0 0 0 1 1
OH -0.676400 0.000000
14 HG1 0 0 0 1 1
HO 0.407000 0.000000
15 C 2 1 0 1 1
C 0.616300 0.000000
16 O 0 0 0 1 1
O -0.572200 0.000000
1 1 2 0 0
0.000000 0.00000E+00
2 1 3 0 0
0.000000 0.00000E+00
3 1 4 0 0
0.000000 0.00000E+00
4 1 5 0 0
0.000000 0.00000E+00
5 5 6 0 0
0.000000 0.00000E+00
6 5 7 0 0
0.000000 0.00000E+00
7 5 15 0 0
0.000000 0.00000E+00
8 7 8 0 0
0.000000 0.00000E+00
9 7 9 0 0
0.000000 0.00000E+00
10 7 13 0 0
0.000000 0.00000E+00
11 9 10 0 0
0.000000 0.00000E+00
12 9 11 0 0
0.000000 0.00000E+00
13 9 12 0 0
0.000000 0.00000E+00
14 13 14 0 0
0.000000 0.00000E+00
15 15 16 0 0
0.000000 0.00000E+00
1 2 1 3 0 0
0.000000 0.00000E+00
2 2 1 4 0 0
0.000000 0.00000E+00
3 2 1 5 0 0
0.000000 0.00000E+00
4 3 1 4 0 0
0.000000 0.00000E+00
5 3 1 5 0 0
0.000000 0.00000E+00
6 4 1 5 0 0
0.000000 0.00000E+00
7 1 5 6 0 0
0.000000 0.00000E+00
8 1 5 7 0 0
0.000000 0.00000E+00
9 1 5 15 0 0
0.000000 0.00000E+00
10 6 5 7 0 0
0.000000 0.00000E+00
11 6 5 15 0 0
0.000000 0.00000E+00
12 7 5 15 0 0
0.000000 0.00000E+00
13 5 7 8 0 0
0.000000 0.00000E+00
14 5 7 9 0 0
0.000000 0.00000E+00
15 5 7 13 0 0
0.000000 0.00000E+00
16 8 7 9 0 0
0.000000 0.00000E+00
17 8 7 13 0 0
0.000000 0.00000E+00
18 9 7 13 0 0
0.000000 0.00000E+00
19 7 9 10 0 0
0.000000 0.00000E+00
20 7 9 11 0 0
0.000000 0.00000E+00
21 7 9 12 0 0
0.000000 0.00000E+00
22 10 9 11 0 0
0.000000 0.00000E+00
23 10 9 12 0 0
0.000000 0.00000E+00
24 11 9 12 0 0
0.000000 0.00000E+00
25 7 13 14 0 0
0.000000 0.00000E+00
26 5 15 16 0 0
0.000000 0.00000E+00
1 2 1 5 6 0 0
0 0.000000 0.00000E+00
2 2 1 5 7 0 0
0 0.000000 0.00000E+00
3 2 1 5 15 0 0
0 0.000000 0.00000E+00
4 3 1 5 6 0 0
0 0.000000 0.00000E+00
5 3 1 5 7 0 0
0 0.000000 0.00000E+00
6 3 1 5 15 0 0
0 0.000000 0.00000E+00
7 4 1 5 6 0 0
0 0.000000 0.00000E+00
8 4 1 5 7 0 0
0 0.000000 0.00000E+00
9 4 1 5 15 0 0
0 0.000000 0.00000E+00
10 1 5 7 8 0 0
0 0.000000 0.00000E+00
11 1 5 7 9 0 0
0 0.000000 0.00000E+00
12 1 5 7 13 0 0
0 0.000000 0.00000E+00
13 6 5 7 8 0 0
0 0.000000 0.00000E+00
14 6 5 7 9 0 0
0 0.000000 0.00000E+00
15 6 5 7 13 0 0
0 0.000000 0.00000E+00
16 15 5 7 8 0 0
0 0.000000 0.00000E+00
17 15 5 7 9 0 0
0 0.000000 0.00000E+00
18 15 5 7 13 0 0
0 0.000000 0.00000E+00
19 1 5 15 16 0 0
0 0.000000 0.00000E+00
20 6 5 15 16 0 0
0 0.000000 0.00000E+00
21 7 5 15 16 0 0
0 0.000000 0.00000E+00
22 5 7 9 10 0 0
0 0.000000 0.00000E+00
23 5 7 9 11 0 0
0 0.000000 0.00000E+00
24 5 7 9 12 0 0
0 0.000000 0.00000E+00
25 8 7 9 10 0 0
0 0.000000 0.00000E+00
26 8 7 9 11 0 0
0 0.000000 0.00000E+00
27 8 7 9 12 0 0
0 0.000000 0.00000E+00
28 13 7 9 10 0 0
0 0.000000 0.00000E+00
29 13 7 9 11 0 0
0 0.000000 0.00000E+00
30 13 7 9 12 0 0
0 0.000000 0.00000E+00
31 5 7 13 14 0 0
0 0.000000 0.00000E+00
32 8 7 13 14 0 0
0 0.000000 0.00000E+00
33 9 7 13 14 0 0
0 0.000000 0.00000E+00

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#
# This is a AMBER test that uses a PDB geometry, and the *.frg files from NWChem to asign atom types
#
Title "big"
memory 3500 Mb
permanent_dir .
echo
prepare
system big
source big.pdb
new_top new_seq
new_rst
amber
vacuo
end
print debug
task prepare
md
system big_md
sd 3000 init 0.001 min 0.000000004 max 0.01
cutoff short 1500 long 1500
shake 1000 0.000001 # Match 0.00001 A in Amber
end
task md energy
task shell "cp big_md.out big_energy.out"
task md optimize

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3.0940000 42.8030000 16.1480000 3.4279009 43.3362088 17.0381119
3.7446931 41.9462510 15.9728418 3.1348291 43.4714304 15.2879808
1.5630000 41.0660000 17.2800000 2.5489704 40.6065641 17.3498694
1.2392446 41.3827483 18.2714396 0.5560000 40.0400000 16.7130000
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-0.4303684 40.4986006 16.6432660 -0.3670000 43.2000000 17.8720000
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-1.7110279 42.3732543 16.6800390 -2.5170000 42.3090000 18.6610000
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-4.5588318 42.4626868 19.1254534 -3.8766979 43.7239870 18.0714375
-4.5160000 41.9640000 17.0540000 -4.0240000 40.9170000 16.5730000
-5.5540000 42.4400000 16.5610000 -2.3650000 40.8170000 19.0550000
-1.5510000 40.1260000 18.4370000 -3.1150000 40.4010000 20.0580000
-3.6505254 41.0491054 20.6177064 -3.0210000 38.9840000 20.5130000
-1.9854985 38.7282991 20.7376172 -3.8620000 38.7930000 21.7870000
-3.5535846 39.4917336 22.5646571 -4.9306561 38.9035154 21.6029876
-3.6610000 37.4020000 22.3500000 -2.3950000 36.9960000 22.7580000
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-3.1908190 33.8473042 23.7154860 -4.6230000 35.2460000 22.9050000
-5.4903283 34.5870160 22.9447715 -4.7580000 36.5450000 22.4270000
-5.7337679 36.9084922 22.1047416 -3.3070000 37.9470000 19.4450000
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-5.4080000 39.1300000 18.9450000 -5.0310577 40.0512827 18.5008683
-5.5959046 39.2894819 20.0067704 -6.6180000 38.5900000 18.2210000
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-6.1210000 37.6480000 17.1730000 -5.9461591 38.1792382 16.2374169
-6.8203147 36.8298953 17.0004797 -4.8150000 37.1060000 17.7080000
-5.0190985 36.1363826 18.1621851 -3.7130000 36.9560000 16.6650000
-3.4270000 35.8250000 16.2350000 -3.0710000 38.0410000 16.2750000
-3.3898602 38.9199052 16.6570380 -1.9810000 38.0650000 15.2770000
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-1.5756776 40.0513214 15.7671775 -0.6052708 39.3855059 14.4322112
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-3.5312388 40.0377872 14.1503466 -2.2530000 41.7000000 13.7060000
-1.4700000 42.2170000 14.4380000 -2.9200000 42.2490000 12.8000000
-0.7470000 37.3510000 15.8140000 -0.1260000 36.5320000 15.1100000
-0.3870000 37.6120000 17.0610000 -0.9224354 38.3152746 17.5496851
0.7440000 36.9900000 17.7580000 1.6556967 37.1629756 17.1861716
0.9300000 37.5630000 19.1540000 1.2431540 38.5990928 19.0253702
-0.0315200 37.5355703 19.6666664 1.9230000 36.9270000 20.0730000
1.5360000 35.8880000 20.9290000 0.5065296 35.5298248 20.9300188
2.4780000 35.3100000 21.7850000 2.1850407 34.4811522 22.4294276
3.7900000 35.7900000 21.8170000 4.5125121 35.3533056 22.5064738
4.1760000 36.8290000 20.9660000 5.1977016 37.2087209 20.9721751
3.2320000 37.3810000 20.1000000 3.5177123 38.1876079 19.4248318
0.5460000 35.4670000 17.8550000 1.5200000 34.7200000 17.6360000
-0.6500000 35.1010000 18.2310000 -1.2808998 35.8462356 18.4892415
-1.0990000 33.7060000 18.4200000 -0.5070283 33.1804220 19.1692906
-2.5330000 33.8040000 18.9150000 -2.3633403 34.5386643 19.7021361
-3.0231382 34.2855066 18.0688227 -3.4060000 32.7050000 19.4380000
-4.3416278 33.1465858 19.7810793 -3.7000000 31.6570000 18.3750000
-2.7648195 31.2146090 18.0317413 -4.3359716 30.8789406 18.7972138
-4.2101408 32.1255564 17.5333874 -2.7450000 32.0620000 20.6570000
-2.6047522 32.8137549 21.4337204 -3.3812843 31.2625026 21.0365358
-1.7769239 31.6505581 20.3712671 -0.8830000 32.9180000 17.1330000
-0.1700000 31.8970000 17.1730000 -1.4580000 33.3930000 16.0430000
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-1.5927128 31.6664337 14.8141499 -2.1650000 33.3640000 13.5620000
-2.3259343 32.5694003 12.8334318 -3.5040000 33.9720000 13.9530000
-3.3438244 34.7670454 14.6812487 -3.9892716 34.3831644 13.0678139
-4.1394211 33.2019319 14.3904194 -1.2710000 34.3300000 12.9300000
-1.7250251 34.7555836 12.1990143 0.1170000 32.5850000 14.2910000
0.4640000 31.5270000 13.7210000 0.9290000 33.5940000 14.5170000
0.5897961 34.4573011 14.9166890 2.3390000 33.5240000 14.1020000
2.3949025 33.0981081 13.1002065 2.9950000 34.8970000 14.0840000
2.6590331 35.4383892 13.1996227 2.6971849 35.4434870 14.9788509
4.5050000 34.7650000 14.0520000 4.8019601 33.7381626 13.8386445
4.9386143 35.4306087 13.3056450 5.1190000 35.2360000 15.7050000
6.5170000 34.1250000 15.9040000 7.2410915 34.3053971 15.1094893
6.9877587 34.3021433 16.8710094 6.1714507 33.0925108 15.8523961
3.1160000 32.5570000 14.9980000 3.9650000 31.7880000 14.5170000
2.8130000 32.6440000 16.2750000 2.1268704 33.3357519 16.5410918
3.4450000 31.8500000 17.3320000 4.5185715 32.0380105 17.3459848
2.8660000 32.2260000 18.6940000 2.7363349 33.3071781 18.7423751
1.8991247 31.7386539 18.8194831 3.7970000 31.7830000 19.7910000
3.4266478 32.0702633 20.7750833 3.9656480 30.7063951 19.7668774
5.3740000 32.6450000 19.4680000 6.3060000 32.1630000 20.9360000
6.3951179 31.0771864 20.9701447 7.3004570 32.6076368 20.8978690
5.7862161 32.5126027 21.8280224 3.2600000 30.3610000 17.0490000
4.1820000 29.5530000 17.2000000 2.0410000 30.0690000 16.6600000
1.3495806 30.8049244 16.6386987 1.6130000 28.7010000 16.3340000
1.8130267 28.0417278 17.1786589 0.1220000 28.6610000 16.0280000
-0.0926107 29.3093637 15.1784903 -0.1729689 27.6394045 15.7883414
-0.4373155 29.0055565 16.8977967 2.4600000 28.1840000 15.1700000
3.2140000 27.2150000 15.3210000 2.3150000 28.8640000 14.0470000
1.6195853 29.5952346 14.0046481 3.0370000 28.5170000 12.8150000
2.7308555 27.5211251 12.4946752 2.7550000 29.5040000 11.6800000
2.7912544 30.5115590 12.0942580 3.5406484 29.3903393 10.9330477
1.3930000 29.2710000 11.0260000 1.1896752 28.2001737 11.0355335
0.6382752 29.7888838 11.6178521 1.3530000 29.7710000 9.6240000
2.2853781 29.4823606 9.1387605 0.5165736 29.2871750 9.1196156
1.1950000 31.2140000 9.5100000 2.0402889 31.7559472 9.4010079
0.0250000 31.8560000 9.5300000 -1.1240000 31.1950000 9.6440000
-1.1184480 30.1876771 9.7172792 -1.9965222 31.7035690 9.6567368
-0.0110000 33.1900000 9.4450000 0.8503955 33.7113265 9.3655232
-0.8994213 33.6701677 9.4606653 4.5230000 28.3770000 13.0940000
5.1770000 27.4790000 12.5260000 5.0380000 29.2340000 13.9550000
4.4689045 29.9577865 14.3701659 6.4590000 29.1810000 14.3060000
7.0273061 29.1604095 13.3761057 6.9530000 30.3450000 15.1520000
6.6315203 31.2648667 14.6635378 6.4750346 30.2665599 16.1284713
8.4760000 30.3660000 15.3290000 8.7022319 30.6903673 16.3447292
8.8562798 29.3557734 15.1775682 9.1340000 31.3060000 14.3410000
9.1644809 32.2898693 14.8091572 10.1511710 30.9456415 14.1873632
8.4300000 31.4040000 13.0120000 7.3749346 31.6073838 13.1952283
8.8666652 32.2302269 12.4509547 8.5630000 30.1510000 12.2300000
8.1580512 29.3853497 12.7495150 8.0809714 30.2517421 11.3481840
9.5405535 29.9625850 12.0597412 6.7500000 27.8840000 15.0730000
7.7960000 27.2570000 14.8140000 6.0009031 27.5098717 15.9726230

17
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initial minimization prior to MD
&cntrl
imin = 1,
maxcyc = 3000,
ncyc = 2000,
ntb = 0,
igb = 6,
cut = 500,
ntmin = 1,
drms = 0.000001,
scee = 1.2,
scnb = 2.0,
nsnb = 1,
ntc=3,
ntf=1
/

5225
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52
QA/amber-tests/big/README Normal file
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This is a series of amino acids
NWChem input files:
big.nw - nwchem input deck
big.pdb - pdb file with geometry
THR_N.sgm - amber95 segment file: one in SVN does not match
amber input files:
big_am.in - amber input deck
big_am.top - amber topology file
big_am.cor - coordinates
NWChem output files:
big.seq
big.nam
VAL.mat
THR.mat
SER.mat
PHE.mat
MET.mat
LEU.mat
ILE.mat
GLU.mat
big.top
big_md.rst
big_md.cmd
big.bsg
ASP.mat
ASN.mat
ARG.mat
ALA.mat
big_energy.out
big.out
big_md.qrs
big_md.out
big.db
amber output files:
mdinfo
big_am.rst
big_am.out
results from *.out files:
4.269883063E+03 kJ/mol for nwchem single point (1.0205d+03 kcal/mol)
-1.36273E+03 for step 500 of nwchem (-3.2570E+02 kcal/mol)
-2.19845E+03 for step 1500 of nwchem (-5.2544E+02 kcal/mol)
-2.63110E+03 for step 3000 of nwchem (-6.2885E+02 kcal/mol)
1.0211E+03 kcal/mol for amber single point
-4.6434E+02 kcal/mol for amber 500 steps
-6.4649E+02 kcal/mol for amber 1500 steps
-7.5345E+02 kcal/mol for amber 3000 steps
Note that this is an unzipping of the amino acid chain, so the energy just keeps dropping

185
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# This file matches the amber force field
# 07/31/09 13:21:28
4.600000
16 15 26 33 0 0 1 1
0.000000
1 N 0 0 0 1 1
N3 0.181200 0.000000
22H 0 0 0 1 1
H 0.193400 0.000000
33H 0 0 0 1 1
H 0.193400 0.000000
44H 0 0 0 1 1
H 0.193400 0.000000
5 CA 0 0 0 1 1
CT 0.003400 0.000000
6 HA 0 0 0 1 1
HP 0.108700 0.000000
7 CB 0 0 0 1 1
CT 0.451400 0.000000
8 HB 0 0 0 1 1
H1 -0.032300 0.000000
9 CG2 0 0 0 1 1
CT -0.255400 0.000000
102HG2 0 0 0 1 1
HC 0.062700 0.000000
113HG2 0 0 0 1 1
HC 0.062700 0.000000
124HG2 0 0 0 1 1
HC 0.062700 0.000000
13 OG1 0 0 0 1 1
OH -0.676400 0.000000
14 HG1 0 0 0 1 1
HO 0.407000 0.000000
15 C 2 1 0 1 1
C 0.616300 0.000000
16 O 0 0 0 1 1
O -0.572200 0.000000
1 1 2 0 0
0.000000 0.00000E+00
2 1 3 0 0
0.000000 0.00000E+00
3 1 4 0 0
0.000000 0.00000E+00
4 1 5 0 0
0.000000 0.00000E+00
5 5 6 0 0
0.000000 0.00000E+00
6 5 7 0 0
0.000000 0.00000E+00
7 5 15 0 0
0.000000 0.00000E+00
8 7 8 0 0
0.000000 0.00000E+00
9 7 9 0 0
0.000000 0.00000E+00
10 7 13 0 0
0.000000 0.00000E+00
11 9 10 0 0
0.000000 0.00000E+00
12 9 11 0 0
0.000000 0.00000E+00
13 9 12 0 0
0.000000 0.00000E+00
14 13 14 0 0
0.000000 0.00000E+00
15 15 16 0 0
0.000000 0.00000E+00
1 2 1 3 0 0
0.000000 0.00000E+00
2 2 1 4 0 0
0.000000 0.00000E+00
3 2 1 5 0 0
0.000000 0.00000E+00
4 3 1 4 0 0
0.000000 0.00000E+00
5 3 1 5 0 0
0.000000 0.00000E+00
6 4 1 5 0 0
0.000000 0.00000E+00
7 1 5 6 0 0
0.000000 0.00000E+00
8 1 5 7 0 0
0.000000 0.00000E+00
9 1 5 15 0 0
0.000000 0.00000E+00
10 6 5 7 0 0
0.000000 0.00000E+00
11 6 5 15 0 0
0.000000 0.00000E+00
12 7 5 15 0 0
0.000000 0.00000E+00
13 5 7 8 0 0
0.000000 0.00000E+00
14 5 7 9 0 0
0.000000 0.00000E+00
15 5 7 13 0 0
0.000000 0.00000E+00
16 8 7 9 0 0
0.000000 0.00000E+00
17 8 7 13 0 0
0.000000 0.00000E+00
18 9 7 13 0 0
0.000000 0.00000E+00
19 7 9 10 0 0
0.000000 0.00000E+00
20 7 9 11 0 0
0.000000 0.00000E+00
21 7 9 12 0 0
0.000000 0.00000E+00
22 10 9 11 0 0
0.000000 0.00000E+00
23 10 9 12 0 0
0.000000 0.00000E+00
24 11 9 12 0 0
0.000000 0.00000E+00
25 7 13 14 0 0
0.000000 0.00000E+00
26 5 15 16 0 0
0.000000 0.00000E+00
1 2 1 5 6 0 0
0 0.000000 0.00000E+00
2 2 1 5 7 0 0
0 0.000000 0.00000E+00
3 2 1 5 15 0 0
0 0.000000 0.00000E+00
4 3 1 5 6 0 0
0 0.000000 0.00000E+00
5 3 1 5 7 0 0
0 0.000000 0.00000E+00
6 3 1 5 15 0 0
0 0.000000 0.00000E+00
7 4 1 5 6 0 0
0 0.000000 0.00000E+00
8 4 1 5 7 0 0
0 0.000000 0.00000E+00
9 4 1 5 15 0 0
0 0.000000 0.00000E+00
10 1 5 7 8 0 0
0 0.000000 0.00000E+00
11 1 5 7 9 0 0
0 0.000000 0.00000E+00
12 1 5 7 13 0 0
0 0.000000 0.00000E+00
13 6 5 7 8 0 0
0 0.000000 0.00000E+00
14 6 5 7 9 0 0
0 0.000000 0.00000E+00
15 6 5 7 13 0 0
0 0.000000 0.00000E+00
16 15 5 7 8 0 0
0 0.000000 0.00000E+00
17 15 5 7 9 0 0
0 0.000000 0.00000E+00
18 15 5 7 13 0 0
0 0.000000 0.00000E+00
19 1 5 15 16 0 0
0 0.000000 0.00000E+00
20 6 5 15 16 0 0
0 0.000000 0.00000E+00
21 7 5 15 16 0 0
0 0.000000 0.00000E+00
22 5 7 9 10 0 0
0 0.000000 0.00000E+00
23 5 7 9 11 0 0
0 0.000000 0.00000E+00
24 5 7 9 12 0 0
0 0.000000 0.00000E+00
25 8 7 9 10 0 0
0 0.000000 0.00000E+00
26 8 7 9 11 0 0
0 0.000000 0.00000E+00
27 8 7 9 12 0 0
0 0.000000 0.00000E+00
28 13 7 9 10 0 0
0 0.000000 0.00000E+00
29 13 7 9 11 0 0
0 0.000000 0.00000E+00
30 13 7 9 12 0 0
0 0.000000 0.00000E+00
31 5 7 13 14 0 0
0 0.000000 0.00000E+00
32 8 7 13 14 0 0
0 0.000000 0.00000E+00
33 9 7 13 14 0 0
0 0.000000 0.00000E+00

32
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#
# This is a AMBER test that uses a PDB geometry, and the *.frg files from NWChem to asign atom types
#
Title "big"
memory 3500 Mb
permanent_dir .
echo
prepare
system big
source big.pdb
new_top new_seq
new_rst
amber
vacuo
end
print debug
task prepare
md
system big_md
sd 3000 init 0.001 min 0.000000004 max 0.05
noshake solvent solute
cutoff short 500 long 500
end
task md energy
task shell "cp big_md.out big_energy.out"
task md optimize

1078
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540
QA/amber-tests/big/big_am.cor Normal file
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1076
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-6.2946862 23.3475465 24.8727927 -8.0087968 23.5550476 24.5915977
-6.8910000 25.1930000 24.4280000 -5.8850703 25.2745585 24.0162320
-7.9230000 25.6260000 23.3230000 -7.8345081 26.7056384 23.2019616
-7.7040000 24.9430000 21.9740000 -7.7928053 23.8632894 22.0941593
-8.4534963 25.2918616 21.2636128 -6.7092326 25.1858804 21.6004395
-9.2380000 25.3860000 23.9080000 -9.9185752 25.6325634 23.2774255
-6.8010000 26.2280000 25.5430000 -5.8290000 26.9990000 25.5610000
-7.7810000 26.2170000 26.4190000 -8.5466857 25.5741995 26.2753607
-7.8580000 27.1540000 27.5570000 -8.1329647 28.1400214 27.1824931
-8.8810000 26.7260000 28.5920000 -9.7307785 26.3972520 27.9937521
-8.4181838 25.8626578 29.0700601 -9.3580000 27.6990000 29.6570000
-8.4615931 28.0538152 30.1655880 -9.8244452 28.5273104 29.1236802
-10.3220000 27.1490000 30.6680000 -10.7750000 26.0340000 30.3340000
-10.6480000 27.7010000 31.7060000 -6.5020000 27.3430000 28.2240000
-6.0400000 28.4830000 28.4230000 -5.8780000 26.2240000 28.5550000
-6.3422524 25.3435754 28.3834728 -4.5540000 26.2010000 29.1940000
-4.5434862 26.8959116 30.0336943 -4.2200000 24.8180000 29.7070000
-4.9839982 24.6501070 30.4660902 -4.4211444 24.1841216 28.8433802
-2.8590000 24.4770000 30.2770000 -2.1496331 24.5751268 29.4552515
-2.6308417 25.2174871 31.0436302 -2.7550000 23.0960000 30.8670000
-3.0960000 22.0690000 30.3040000 -2.2840000 23.1150000 32.0290000
-3.4880000 26.6540000 28.1940000 -2.4920000 27.2840000 28.5750000
-3.7420000 26.3350000 26.9340000 -4.5632789 25.7725947 26.7628262
-2.8740000 26.6630000 25.7970000 -1.8532639 26.3764321 26.0501323
-3.2730000 25.9550000 24.5100000 -4.3625372 25.9292851 24.4913794
-2.9105382 26.5718993 23.6877125 -2.7310000 24.5440000 24.3610000
-1.6569867 24.5496612 24.5469148 -3.2233721 23.9090851 25.0975832
-2.9800000 23.9700000 22.9850000 -4.0820000 23.8580000 22.4520000
-1.8930000 23.5810000 22.3350000 -1.9761311 23.1864487 21.4089763
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-5.4951060 31.6448304 24.4388734 -6.4410000 29.6970000 24.2310000
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-3.5680000 30.3860000 27.6410000 -4.2157133 29.6183928 27.7475173
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-1.4270000 31.0940000 28.6770000 -0.8490000 32.1200000 29.0600000
-0.7870000 30.0840000 28.1070000 -1.2993264 29.2576866 27.8334544
0.6700000 30.1020000 27.9000000 1.1638343 30.3981376 28.8254887
1.1910000 28.7180000 27.4870000 0.7371114 28.4606583 26.5299944
2.2722547 28.7883350 27.3685037 0.8590000 27.6300000 28.5200000
1.3569297 27.9177537 29.4459399 -0.2209283 27.6562455 28.6654830
1.2770000 26.2450000 28.1390000 2.4510000 26.0280000 28.5170000
0.5840000 25.4400000 27.5470000 1.0980000 31.1160000 26.8520000
2.1830000 31.7040000 26.9570000 0.2230000 31.2830000 25.8790000
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1.5117698 32.1719031 24.4906886 -0.3930000 31.9690000 23.5500000
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0.0660000 30.8670000 22.6410000 1.3280000 30.9200000 22.0460000
1.9859561 31.7643528 22.2515773 1.7520000 29.8910000 21.1850000
2.7360664 29.9255917 20.7175415 0.8930000 28.8130000 20.9310000
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15
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@ -0,0 +1,15 @@
initial minimization prior to MD
&cntrl
imin = 1,
maxcyc = 3000,
ncyc = 3500,
ntb = 0,
igb = 6,
cut = 500,
ntmin = 1,
drms = 0.000001,
scee = 1.2,
scnb = 2.0,
nsnb = 1
/

5225
QA/amber-tests/big/big_am.top Normal file
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File diff suppressed because it is too large Load diff

68
QA/amber-tests/dotests.msub Normal file
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#!/bin/csh -f
#MSUB -A mscfcons
#MSUB -l nodes=1:ppn=8,walltime=30:00
#MSUB -e test.out.%j
#MSUB -o test.out.%j
#MSUB -N NWChemAmber
### If you do this as a bash shell then NWChem gives bogus errors at completion related the the task system calls
source /etc/profile.d/modules.csh
source /home/scicons/bin/set_modulepath.csh
module purge
module load amber/10
setenv AMBEREXE ${AMBERHOME}/bin/sander.MPI
setenv DOAMBER "srun --mpi=none -n 1 -N 1 ${AMBEREXE}"
cd big
${DOAMBER} -O -i big_am.in -o big_am.out -p big_am.top -c big_am.cor -r big_am.rst
cd ..
cd big.shake
${DOAMBER} -O -i big_am.in -o big_am.out -p big_am.top -c big_am.cor -r big_am.rst
cd ..
cd ethane
${DOAMBER} -O -i eth_am.in -o eth_am.out -p eth_am.top -c eth_am.cor -r eth_am.rst
cd ..
cd ethane+
${DOAMBER} -O -i ethplus_am.in -o ethplus_am.out -p ethplus_am.top -c ethplus_am.cor -r ethplus_am.rst
cd ..
cd small
${DOAMBER} -O -i small_am.in -o small_am.out -p small_am.top -c small_am.cor -r small_am.rst
cd ..
module purge
module load nwchem
setenv NWCHEMEXE ${NWCHEM_TOP}/bin/${NWCHEM_TARGET}/nwchem
setenv DONWCHEM "mpirun -srun -n 1 -N 1 ${NWCHEMEXE}"
cd big
${DONWCHEM} big.nw >& big.out
cd ..
cd big.shake
${DONWCHEM} big.nw >& big.out
cd ..
cd ethane
${DONWCHEM} eth.nw >& eth.out
cd ..
cd ethane+
${DONWCHEM} ethplus.nw >& ethplus.out
cd ../
cd small
${DONWCHEM} small.nw >& small.out
cd ..
cd methanol
${DONWCHEM} meoh.nw >& meoh.out
cd ..

47
QA/amber-tests/ethane+/README Normal file
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This is an Ethane 4 plus ion, that NWChem generates new data for
NWChem input file:
ethplus.nw - nwchem input deck
Amber input files:
ethplus_am.in - amber input deck
ethplus_am.cor - coordinates
ethplus_am.top - topology file
NWChem output files:
ethplus.zmat
ethplus.p
ethplus.nam
ethplus.movecs
ethplus.c
ethplus.b^-1
ethplus.b
ethplus.xyz
ethplus.top
ethplus.seq
ethplus.q
ethplus.plt
ethplus_md.rst
ethplus_md.cmd
ethplus.grid
ethplus_energy.out
ethplus.bsg
ethpl.sgm
ethpl.frg
ethplus.out
ethplus_md.qrs
ethplus_md.out
ethplus.db
Amber output files:
mdinfo
ethplus_am.rst
ethplus_am.out
Results from *.out files:
1.471673291E+03 kJ/mol NWChem single point (3.5174E+02 kcal/mol)
1.38277E+03 kJ/mol NWChem step 25 (3.3049E+02 kcal/mol)
3.5181E+02 kcal/mol Amber single point
3.3048E+02 kcal/mol Amber step 400
Note that NWChem and Amber match both optimized and initial

57
QA/amber-tests/ethane+/ethplus.nw Normal file
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#
# This is an AMBER test that uses a NWChem geometry
# It is uses the automatic atom type determination at the end of the Amber force file
#
Title "ethane plus"
memory 3000 Mb
permanent_dir .
start ethplus
echo
charge +4
geometry autosym
H -0.97624726 -0.26158466 -1.15438725
H 0.71466259 -0.71466259 -1.15438725
H 0.26158466 0.97624726 -1.15438725
C 0.00000000 0.00000000 -0.76221612
C 0.00000000 0.00000000 0.76221612
H -0.71466259 0.71466259 1.15438725
H -0.26158466 -0.97624726 1.15438725
H 0.97624726 0.26158466 1.15438725
end
basis
* library sto-3g
end
task scf
esp
constrain equal 1 2 3 6 7 8
constrain equal 4 5
end
prepare
source rtdb
amber
new_top new_seq
new_rst
# write pdb ethplus.pdb
vacuo
end
task prepare
md
system ethplus_md
noshake solvent solute
end
task md energy
task shell "cp ethplus_md.out ethplus_energy.out"
task md optimize

6
QA/amber-tests/ethane+/ethplus_am.cor Normal file
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@ -0,0 +1,6 @@
8
-0.7150000 0.7150000 1.1540000 0.9760000 0.2620000 1.1540000
-0.2620000 -0.9760000 1.1540000 0.0000000 0.0000000 0.7620000
0.0000000 0.0000000 -0.7620000 -0.9760000 -0.2620000 -1.1540000
0.2620000 0.9760000 -1.1540000 0.7150000 -0.7150000 -1.1540000

12
QA/amber-tests/ethane+/ethplus_am.in Normal file
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initial minimization prior to MD
&cntrl
imin = 1,
maxcyc = 400,
ncyc = 400,
ntb = 0,
igb = 0,
cut = 50
ntmin = 1
drms = 0.000001
/

130
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%VERSION VERSION_STAMP = V0001.000 DATE = 07/31/09 09:02:17
%FLAG TITLE
%FORMAT(20a4)
%FLAG POINTERS
%FORMAT(10I8)
8 2 6 1 12 0 9 0 0 0
29 1 1 0 0 2 2 1 2 0
0 0 0 0 0 0 0 0 8 0
0
%FLAG ATOM_NAME
%FORMAT(20a4)
H12 H13 H14 C1 C5 H22 H23 H24
%FLAG CHARGE
%FORMAT(5E16.8)
1.12008834E+01 1.12008834E+01 1.12008834E+01 2.84196813E+00 2.84196813E+00
1.12008834E+01 1.12008834E+01 1.12008834E+01
%FLAG MASS
%FORMAT(5E16.8)
1.00800000E+00 1.00800000E+00 1.00800000E+00 1.20100000E+01 1.20100000E+01
1.00800000E+00 1.00800000E+00 1.00800000E+00
%FLAG ATOM_TYPE_INDEX
%FORMAT(10I8)
1 1 1 2 2 1 1 1
%FLAG NUMBER_EXCLUDED_ATOMS
%FORMAT(10I8)
7 6 5 4 3 2 1 1
%FLAG NONBONDED_PARM_INDEX
%FORMAT(10I8)
1 2 2 3
%FLAG RESIDUE_LABEL
%FORMAT(20a4)
ETH
%FLAG RESIDUE_POINTER
%FORMAT(10I8)
1
%FLAG BOND_FORCE_CONSTANT
%FORMAT(5E16.8)
3.40000000E+02 3.10000000E+02
%FLAG BOND_EQUIL_VALUE
%FORMAT(5E16.8)
1.09000000E+00 1.52600000E+00
%FLAG ANGLE_FORCE_CONSTANT
%FORMAT(5E16.8)
5.00000000E+01 3.50000000E+01
%FLAG ANGLE_EQUIL_VALUE
%FORMAT(5E16.8)
1.91113635E+00 1.91113635E+00
%FLAG DIHEDRAL_FORCE_CONSTANT
%FORMAT(5E16.8)
1.50000000E-01
%FLAG DIHEDRAL_PERIODICITY
%FORMAT(5E16.8)
3.00000000E+00
%FLAG DIHEDRAL_PHASE
%FORMAT(5E16.8)
0.00000000E+00
%FLAG SOLTY
%FORMAT(5E16.8)
0.00000000E+00 0.00000000E+00
%FLAG LENNARD_JONES_ACOEF
%FORMAT(5E16.8)
7.51607703E+03 9.71708117E+04 1.04308023E+06
%FLAG LENNARD_JONES_BCOEF
%FORMAT(5E16.8)
2.17257828E+01 1.26919150E+02 6.75612247E+02
%FLAG BONDS_INC_HYDROGEN
%FORMAT(10I8)
0 9 1 3 9 1 6 9 1 12
21 1 12 18 1 12 15 1
%FLAG BONDS_WITHOUT_HYDROGEN
%FORMAT(10I8)
9 12 2
%FLAG ANGLES_INC_HYDROGEN
%FORMAT(10I8)
0 9 12 1 0 9 6 2 0 9
3 2 3 9 12 1 3 9 6 2
6 9 12 1 9 12 21 1 9 12
18 1 9 12 15 1 15 12 21 2
15 12 18 2 18 12 21 2
%FLAG ANGLES_WITHOUT_HYDROGEN
%FORMAT(10I8)
%FLAG DIHEDRALS_INC_HYDROGEN
%FORMAT(10I8)
0 9 12 21 1 0 9 12 18 1
0 9 12 15 1 3 9 12 21 1
3 9 12 18 1 3 9 12 15 1
6 9 12 21 1 6 9 12 18 1
6 9 12 15 1
%FLAG DIHEDRALS_WITHOUT_HYDROGEN
%FORMAT(10I8)
%FLAG EXCLUDED_ATOMS_LIST
%FORMAT(10I8)
2 3 4 5 6 7 8 3 4 5
6 7 8 4 5 6 7 8 5 6
7 8 6 7 8 7 8 8 0
%FLAG HBOND_ACOEF
%FORMAT(5E16.8)
%FLAG HBOND_BCOEF
%FORMAT(5E16.8)
%FLAG HBCUT
%FORMAT(5E16.8)
%FLAG AMBER_ATOM_TYPE
%FORMAT(20a4)
HC HC HC CT CT HC HC HC
%FLAG TREE_CHAIN_CLASSIFICATION
%FORMAT(20a4)
BLA BLA BLA BLA BLA BLA BLA BLA
%FLAG JOIN_ARRAY
%FORMAT(10I8)
0 0 0 0 0 0 0 0
%FLAG IROTAT
%FORMAT(10I8)
0 0 0 0 0 0 0 0
%FLAG RADIUS_SET
%FORMAT(1a80)
modified Bondi radii (mbondi)
%FLAG RADII
%FORMAT(5E16.8)
1.30000000E+00 1.30000000E+00 1.30000000E+00 1.70000000E+00 1.70000000E+00
1.30000000E+00 1.30000000E+00 1.30000000E+00
%FLAG SCREEN
%FORMAT(5E16.8)
8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01 7.20000000E-01
8.50000000E-01 8.50000000E-01 8.50000000E-01

47
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This is an Ethane molecule, that NWChem generates new data for
NWChem input file:
eth.nw - nwchem input deck
Amber input files:
eth_am.in - amber input deck
eth_am.cor - coordinates
eth_am.top - topology file
NWChem output files:
-rw-rw-r-- 1 d3p852 d3p852 248 Oct 19 14:12 eth.zmat
-rw-rw-r-- 1 d3p852 d3p852 6.2K Oct 19 14:12 eth.p
-rw-rw-r-- 1 d3p852 d3p852 6.2K Oct 19 14:12 eth.c
-rw-rw-r-- 1 d3p852 d3p852 5.3K Oct 19 14:12 eth.b^-1
-rw-rw-r-- 1 d3p852 d3p852 5.3K Oct 19 14:12 eth.b
-rw-rw-r-- 1 d3p852 d3p852 803 Oct 19 14:12 eth.q
-rw-rw-r-- 1 d3p852 d3p852 104 Oct 19 14:12 eth.nam
-rw-rw-r-- 1 d3p852 d3p852 2.7K Oct 19 14:12 eth.movecs
-rw-rw-r-- 1 d3p852 d3p852 167K Oct 19 14:12 eth.grid
-rw-rw-r-- 1 d3p852 d3p852 442 Oct 19 14:12 eth.xyz
-rw-rw-r-- 1 d3p852 d3p852 4.7K Oct 19 14:12 eth.top
-rw-rw-r-- 1 d3p852 d3p852 2.3K Oct 19 14:12 eth.sgm
-rw-rw-r-- 1 d3p852 d3p852 40 Oct 19 14:12 eth.seq
-rw-rw-r-- 1 d3p852 d3p852 169K Oct 19 14:12 eth.plt
-rw-rw-r-- 1 d3p852 d3p852 41K Oct 19 14:12 eth.out
-rw-rw-r-- 1 d3p852 d3p852 1.3K Oct 19 14:12 eth_md.rst
-rw-rw-r-- 1 d3p852 d3p852 20K Oct 19 14:12 eth_md.qrs
-rw-rw-r-- 1 d3p852 d3p852 9.6K Oct 19 14:12 eth_md.out
-rw-rw-r-- 1 d3p852 d3p852 0 Oct 19 14:12 eth_md.cmd
-rw-rw-r-- 1 d3p852 d3p852 824 Oct 19 14:12 eth.frg
-rw-rw-r-- 1 d3p852 d3p852 12K Oct 19 14:12 eth_energy.out
-rw-rw-r-- 1 d3p852 d3p852 1.1M Oct 19 14:12 eth.db
-rw-rw-r-- 1 d3p852 d3p852 426 Oct 19 14:12 eth.bsg
Amber output files:
-rw-rw-r-- 1 d3p852 d3p852 384 Oct 19 14:11 mdinfo
-rw-rw-r-- 1 d3p852 d3p852 303 Oct 19 14:11 eth_am.rst
-rw-rw-r-- 1 d3p852 d3p852 13K Oct 19 14:11 eth_am.out
Results from *.out files:
3.714703721E+00 kJ/mol Single point energy NWChem (8.8784E-01 kcal/mol)
1.63128E+00 kJ/mol after 19 steps in NWChem (3.8989E-01 kcal/mol)
8.8371E-01 kcal/mol single point energy Amber
3.8987E-01 kcal/mol after 500 steps in Amber
Note that NWChem and Amber match both optimized and initial

54
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#
# This is an AMBER test that uses a NWChem geometry
# It is uses the automatic atom type determination at the end of the Amber force file
#
Title "ethane"
memory 3000 Mb
permanent_dir .
start eth
echo
geometry autosym
H -0.97624726 -0.26158466 -1.15438725
H 0.71466259 -0.71466259 -1.15438725
H 0.26158466 0.97624726 -1.15438725
C 0.00000000 0.00000000 -0.76221612
C 0.00000000 0.00000000 0.76221612
H -0.71466259 0.71466259 1.15438725
H -0.26158466 -0.97624726 1.15438725
H 0.97624726 0.26158466 1.15438725
end
basis
* library sto-3g
end
task scf
esp
constrain equal 1 2 3 6 7 8
constrain equal 4 5
end
prepare
source rtdb
amber
new_top new_seq
new_rst
# write pdb eth.pdb
end
task prepare
md
system eth_md
noshake solvent solute
end
task md energy
task shell "cp eth_md.out eth_energy.out"
task md optimize

14
QA/amber-tests/ethane/eth.pdb Normal file
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@ -0,0 +1,14 @@
HEADER
TITLE THIS IS ETHANE
REMARK 4 XXXX COMPLIES WITH FORMAT V. 2.1, 25-OCT-1996
CRYST1 1.952 1.952 2.309 90.00 90.00 90.00
ATOM 1 2H1 ETH 1 -0.715 0.715 1.154 0.00 H
ATOM 2 3H1 ETH 1 0.976 0.262 1.154 0.00 H
ATOM 3 4H1 ETH 1 -0.262 -0.976 1.154 0.00 H
ATOM 4 C1 ETH 1 0.000 0.000 0.762 0.00 C
ATOM 5 C2 ETH 1 0.000 0.000 -0.762 0.00 C
ATOM 6 2H2 ETH 1 -0.976 -0.262 -1.154 0.00 H
ATOM 7 3H2 ETH 1 0.262 0.976 -1.154 0.00 H
ATOM 8 4H2 ETH 1 0.715 -0.715 -1.154 0.00 H
TER
END

6
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8
-0.7150000 0.7150000 1.1540000 0.9760000 0.2620000 1.1540000
-0.2620000 -0.9760000 1.1540000 0.0000000 0.0000000 0.7620000
0.0000000 0.0000000 -0.7620000 -0.9760000 -0.2620000 -1.1540000
0.2620000 0.9760000 -1.1540000 0.7150000 -0.7150000 -1.1540000

12
QA/amber-tests/ethane/eth_am.in Normal file
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initial minimization prior to MD
&cntrl
imin = 1,
maxcyc = 700,
ncyc = 500,
ntb = 0,
igb = 0,
cut = 50
ntmin = 1
drms = 0.000001
/

130
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%VERSION VERSION_STAMP = V0001.000 DATE = 07/14/09 15:01:10
%FLAG TITLE
%FORMAT(20a4)
%FLAG POINTERS
%FORMAT(10I8)
8 2 6 1 12 0 9 0 0 0
29 1 1 0 0 2 2 1 2 0
0 0 0 0 0 0 0 0 8 0
0
%FLAG ATOM_NAME
%FORMAT(20a4)
H12 H13 H14 C1 C5 H22 H23 H24
%FLAG CHARGE
%FORMAT(5E16.8)
3.11674219E-01 3.11674219E-01 3.11674219E-01 -9.35040880E-01 -9.35040880E-01
3.11674219E-01 3.11674219E-01 3.11674219E-01
%FLAG MASS
%FORMAT(5E16.8)
1.00800000E+00 1.00800000E+00 1.00800000E+00 1.20100000E+01 1.20100000E+01
1.00800000E+00 1.00800000E+00 1.00800000E+00
%FLAG ATOM_TYPE_INDEX
%FORMAT(10I8)
1 1 1 2 2 1 1 1
%FLAG NUMBER_EXCLUDED_ATOMS
%FORMAT(10I8)
7 6 5 4 3 2 1 1
%FLAG NONBONDED_PARM_INDEX
%FORMAT(10I8)
1 2 2 3
%FLAG RESIDUE_LABEL
%FORMAT(20a4)
ETH
%FLAG RESIDUE_POINTER
%FORMAT(10I8)
1
%FLAG BOND_FORCE_CONSTANT
%FORMAT(5E16.8)
3.40000000E+02 3.10000000E+02
%FLAG BOND_EQUIL_VALUE
%FORMAT(5E16.8)
1.09000000E+00 1.52600000E+00
%FLAG ANGLE_FORCE_CONSTANT
%FORMAT(5E16.8)
5.00000000E+01 3.50000000E+01
%FLAG ANGLE_EQUIL_VALUE
%FORMAT(5E16.8)
1.91113635E+00 1.91113635E+00
%FLAG DIHEDRAL_FORCE_CONSTANT
%FORMAT(5E16.8)
1.50000000E-01
%FLAG DIHEDRAL_PERIODICITY
%FORMAT(5E16.8)
3.00000000E+00
%FLAG DIHEDRAL_PHASE
%FORMAT(5E16.8)
0.00000000E+00
%FLAG SOLTY
%FORMAT(5E16.8)
0.00000000E+00 0.00000000E+00
%FLAG LENNARD_JONES_ACOEF
%FORMAT(5E16.8)
7.51607703E+03 9.71708117E+04 1.04308023E+06
%FLAG LENNARD_JONES_BCOEF
%FORMAT(5E16.8)
2.17257828E+01 1.26919150E+02 6.75612247E+02
%FLAG BONDS_INC_HYDROGEN
%FORMAT(10I8)
0 9 1 3 9 1 6 9 1 12
21 1 12 15 1 12 18 1
%FLAG BONDS_WITHOUT_HYDROGEN
%FORMAT(10I8)
9 12 2
%FLAG ANGLES_INC_HYDROGEN
%FORMAT(10I8)
0 9 12 1 0 9 6 2 0 9
3 2 3 9 12 1 3 9 6 2
6 9 12 1 9 12 21 1 9 12
15 1 9 12 18 1 15 12 21 2
15 12 18 2 18 12 21 2
%FLAG ANGLES_WITHOUT_HYDROGEN
%FORMAT(10I8)
%FLAG DIHEDRALS_INC_HYDROGEN
%FORMAT(10I8)
0 9 12 21 1 0 9 12 15 1
0 9 12 18 1 3 9 12 21 1
3 9 12 15 1 3 9 12 18 1
6 9 12 21 1 6 9 12 15 1
6 9 12 18 1
%FLAG DIHEDRALS_WITHOUT_HYDROGEN
%FORMAT(10I8)
%FLAG EXCLUDED_ATOMS_LIST
%FORMAT(10I8)
2 3 4 5 6 7 8 3 4 5
6 7 8 4 5 6 7 8 5 6
7 8 6 7 8 7 8 8 0
%FLAG HBOND_ACOEF
%FORMAT(5E16.8)
%FLAG HBOND_BCOEF
%FORMAT(5E16.8)
%FLAG HBCUT
%FORMAT(5E16.8)
%FLAG AMBER_ATOM_TYPE
%FORMAT(20a4)
HC HC HC CT CT HC HC HC
%FLAG TREE_CHAIN_CLASSIFICATION
%FORMAT(20a4)
BLA BLA BLA BLA BLA BLA BLA BLA
%FLAG JOIN_ARRAY
%FORMAT(10I8)
0 0 0 0 0 0 0 0
%FLAG IROTAT
%FORMAT(10I8)
0 0 0 0 0 0 0 0
%FLAG RADIUS_SET
%FORMAT(1a80)
modified Bondi radii (mbondi)
%FLAG RADII
%FORMAT(5E16.8)
1.30000000E+00 1.30000000E+00 1.30000000E+00 1.70000000E+00 1.70000000E+00
1.30000000E+00 1.30000000E+00 1.30000000E+00
%FLAG SCREEN
%FORMAT(5E16.8)
8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01 7.20000000E-01
8.50000000E-01 8.50000000E-01 8.50000000E-01

21
QA/amber-tests/methanol/README Normal file
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@ -0,0 +1,21 @@
This is a solvent only NWChem run
NWChem input files:
meoh.nw - nwchem input deck
meoh.pdb - EMPTY pdb file, to fool nwchem
meoh.rst - restart file - same as scr/data/solvents/meoh.rst
NWChem output files:
meoh.top
meoh.seq
meoh_out.pdb - This is a PDB file of the resulting structure
meoh.out
meoh.nam
meoh_em.rst
meoh.db
meoh.bsg
Result:
Expect a 5780 line PDB file that starts like
CRYST1 42.476 42.476 42.476 90.00 90.00 90.00
Note that this is not a test of a result, it is a functionality test

33
QA/amber-tests/methanol/meoh.nw Normal file
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#
# This is a test of a Solvent Only run
# The meoh.pdb file is empty, because NWChem needs a solute
# This uses the segment file provided with NWChem
#
Title "solvent methanol"
memory 1800 Mb
permanent_dir .
start meoh
echo
basis
* library sto-3g
end
prepare
amber
source pdb
read rst meoh.rst
system meoh_em
solvent name MOH model meoh
touch 0.25
expand 0.1
center
solvate
new_top new_seq
new_rst
write pdb meoh_out.pdb
end
task prepare

2
QA/amber-tests/methanol/meoh.pdb Normal file
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@ -0,0 +1,2 @@
REMARK EMPTY PDB FILE
END

1741
QA/amber-tests/methanol/meoh.rst Normal file
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File diff suppressed because it is too large Load diff

37
QA/amber-tests/small/README Normal file
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@ -0,0 +1,37 @@
This is an ALA dimer
NWChem input files:
small.nw - nwchem job file
small.pdb - geometry as a PDB file, used by small.nw
NWChem output file:
small_energy.out
small_md.out
small.top
small.seq
small.out
small.nam
small_md.rst
small_md.qrs
small_md.cmd
small.db
small.bsg
Amber input files:
small_am.in - amber job file
small_am.cor - amber coordinate file
small_am.top - amber topology file
Amber output files:
small_am.out
small_am.rst
mdinfo
Results from *.out files:
-1.374134919E+02 kJ/mol for single point NWChem (-3.2843E+01 kcal/mol)
-1.83007E+02 kJ/mol for 500 steps NWChem (-4.3740E+01 kcal/mol)
-1.90732E+02 kj/mol for 7000 steps NWChem (-4.5586E+01 kcal/mol)
-3.2847E+01 kcal/mol for single point Amber
-4.5025E+01 kcal/mol for 500 steps Amber
-4.5867E+01 kcal/mol for 7000 steps Amber
Note that the initial and optimized energies match well

33
QA/amber-tests/small/small.nw Normal file
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#
# This is a amber test that uses a PDB geometry
#
Title "small"
memory 3500 Mb
permanent_dir .
# use the next line to verify that all atoms are really found
# print debug
echo
prepare
system small
source small.pdb
new_top new_seq
new_rst
amber
vacuo
end
print debug
task prepare
md
system small_md
sd 7000 init 0.001 min 0.000000001 max 0.05
noshake solvent solute
end
task md energy
task shell "cp small_md.out small_energy.out"
task md optimize

25
QA/amber-tests/small/small.pdb Normal file
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ATOM 1 N ALA 1 -0.491 0.404 1.207 1.00 0.00
ATOM 2 2H ALA 1 -1.404 0.049 1.455 1.00 0.00
ATOM 3 3H ALA 1 0.141 0.360 1.994 1.00 0.00
ATOM 4 4H ALA 1 -0.544 1.373 0.924 1.00 0.00
ATOM 5 CA ALA 1 0.112 -0.360 0.098 1.00 0.00
ATOM 6 HA ALA 1 -0.506 -0.224 -0.791 1.00 0.00
ATOM 7 CB ALA 1 0.185 -1.856 0.423 1.00 0.00
ATOM 8 2HB ALA 1 0.769 -2.016 1.330 1.00 0.00
ATOM 9 3HB ALA 1 0.650 -2.395 -0.404 1.00 0.00
ATOM 10 4HB ALA 1 -0.819 -2.256 0.576 1.00 0.00
ATOM 11 C ALA 1 1.501 0.207 -0.184 1.00 0.00
ATOM 12 O ALA 1 1.862 1.202 0.441 1.00 0.00
ATOM 13 N ALA 2 2.246 -0.417 -1.094 1.00 0.00
ATOM 14 H ALA 2 1.869 -1.205 -1.607 1.00 0.00
ATOM 15 CA ALA 2 3.541 0.027 -1.590 1.00 0.00
ATOM 16 HA ALA 2 4.313 -0.337 -0.910 1.00 0.00
ATOM 17 CB ALA 2 3.608 1.556 -1.663 1.00 0.00
ATOM 18 2HB ALA 2 2.830 1.929 -2.330 1.00 0.00
ATOM 19 3HB ALA 2 4.585 1.870 -2.032 1.00 0.00
ATOM 20 4HB ALA 2 3.454 1.974 -0.668 1.00 0.00
ATOM 21 C ALA 2 3.746 -0.574 -2.985 1.00 0.00
ATOM 22 O ALA 2 4.786 -0.260 -3.601 1.00 0.00
ATOM 23 OXT ALA 2 2.844 -1.340 -3.399 1.00 0.00
TER
END

14
QA/amber-tests/small/small_am.cor Normal file
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@ -0,0 +1,14 @@
23
-0.4910000 0.4040000 1.2070000 -1.4040000 0.0490000 1.4550000
0.1410000 0.3600000 1.9940000 -0.5440000 1.3730000 0.9240000
0.1120000 -0.3600000 0.0980000 -0.5060000 -0.2240000 -0.7910000
0.1850000 -1.8560000 0.4230000 0.7690000 -2.0160000 1.3300000
0.6500000 -2.3950000 -0.4040000 -0.8190000 -2.2560000 0.5760000
1.5010000 0.2070000 -0.1840000 1.8620000 1.2020000 0.4410000
2.2460000 -0.4170000 -1.0940000 1.8690000 -1.2050000 -1.6070000
3.5410000 0.0270000 -1.5900000 4.3130000 -0.3370000 -0.9100000
3.6080000 1.5560000 -1.6630000 2.8300000 1.9290000 -2.3300000
4.5850000 1.8700000 -2.0320000 3.4540000 1.9740000 -0.6680000
3.7460000 -0.5740000 -2.9850000 4.7860000 -0.2600000 -3.6010000
2.8440000 -1.3400000 -3.3990000

12
QA/amber-tests/small/small_am.in Normal file
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@ -0,0 +1,12 @@
initial minimization prior to MD
&cntrl
imin = 1,
maxcyc = 7000,
ncyc = 3500,
ntb = 0,
igb = 0,
cut = 50
ntmin = 1
drms = 0.000001
/

240
QA/amber-tests/small/small_am.top Normal file
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@ -0,0 +1,240 @@
%VERSION VERSION_STAMP = V0001.000 DATE = 07/13/09 12:33:19
%FLAG TITLE
%FORMAT(20a4)
%FLAG POINTERS
%FORMAT(10I8)
23 8 12 10 26 13 39 19 0 0
111 2 10 13 19 12 23 13 10 0
0 0 0 0 0 0 0 0 12 0
0
%FLAG ATOM_NAME
%FORMAT(20a4)
N H1 H2 H3 CA HA CB HB1 HB2 HB3 C O N H CA HA CB HB1 HB2 HB3
C O OXT
%FLAG CHARGE
%FORMAT(5E16.8)
2.57663322E+00 3.63899331E+00 3.63899331E+00 3.63899331E+00 1.75298526E+00
1.61996247E+00 -1.08787131E+00 5.46669000E-01 5.46669000E-01 5.46669000E-01
1.12304035E+01 -1.04268001E+01 -6.96274083E+00 4.88539863E+00 -3.18343581E+00
1.94431941E+00 -3.81392739E+00 1.39218372E+00 1.39218372E+00 1.39218372E+00
1.40876601E+01 -1.46780627E+01 -1.46780627E+01
%FLAG MASS
%FORMAT(5E16.8)
1.40100000E+01 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.20100000E+01
1.00800000E+00 1.20100000E+01 1.00800000E+00 1.00800000E+00 1.00800000E+00
1.20100000E+01 1.60000000E+01 1.40100000E+01 1.00800000E+00 1.20100000E+01
1.00800000E+00 1.20100000E+01 1.00800000E+00 1.00800000E+00 1.00800000E+00
1.20100000E+01 1.60000000E+01 1.60000000E+01
%FLAG ATOM_TYPE_INDEX
%FORMAT(10I8)
1 2 2 2 3 4 3 5 5 5
6 7 1 2 3 8 3 5 5 5
6 7 7
%FLAG NUMBER_EXCLUDED_ATOMS
%FORMAT(10I8)
12 6 5 4 10 7 6 3 2 1
7 3 10 4 8 7 6 3 2 1
2 1 1
%FLAG NONBONDED_PARM_INDEX
%FORMAT(10I8)
1 2 4 7 11 16 22 29 2 3
5 8 12 17 23 30 4 5 6 9
13 18 24 31 7 8 9 10 14 19
25 32 11 12 13 14 15 20 26 33
16 17 18 19 20 21 27 34 22 23
24 25 26 27 28 35 29 30 31 32
33 34 35 36
%FLAG RESIDUE_LABEL
%FORMAT(20a4)
ALA ALA
%FLAG RESIDUE_POINTER
%FORMAT(10I8)
1 13
%FLAG BOND_FORCE_CONSTANT
%FORMAT(5E16.8)
5.70000000E+02 4.90000000E+02 3.40000000E+02 3.40000000E+02 3.10000000E+02
3.17000000E+02 4.34000000E+02 3.67000000E+02 6.56000000E+02 3.40000000E+02
4.34000000E+02 3.37000000E+02
%FLAG BOND_EQUIL_VALUE
%FORMAT(5E16.8)
1.22900000E+00 1.33500000E+00 1.09000000E+00 1.09000000E+00 1.52600000E+00
1.52200000E+00 1.01000000E+00 1.47100000E+00 1.25000000E+00 1.09000000E+00
1.01000000E+00 1.44900000E+00
%FLAG ANGLE_FORCE_CONSTANT
%FORMAT(5E16.8)
8.00000000E+01 5.00000000E+01 5.00000000E+01 3.50000000E+01 6.30000000E+01
5.00000000E+01 5.00000000E+01 5.00000000E+01 8.00000000E+01 7.00000000E+01
5.00000000E+01 3.50000000E+01 5.00000000E+01 8.00000000E+01 8.00000000E+01
8.00000000E+01 5.00000000E+01 5.00000000E+01 7.00000000E+01 5.00000000E+01
5.00000000E+01 8.00000000E+01 6.30000000E+01
%FLAG ANGLE_EQUIL_VALUE
%FORMAT(5E16.8)
2.14501057E+00 2.09439600E+00 2.12755727E+00 1.91113635E+00 1.93906163E+00
1.91113635E+00 1.91113635E+00 1.91113635E+00 2.10137732E+00 2.03505478E+00
1.91113635E+00 1.91113635E+00 1.91113635E+00 1.94080696E+00 1.94080696E+00
2.19911580E+00 1.91113635E+00 1.91113635E+00 2.04203610E+00 2.06018753E+00
1.91113635E+00 1.91462701E+00 1.92160833E+00
%FLAG DIHEDRAL_FORCE_CONSTANT
%FORMAT(5E16.8)
2.00000000E+00 2.50000000E+00 0.00000000E+00 5.30000000E-01 1.50000000E-01
5.00000000E-01 8.00000000E-01 8.50000000E-01 1.55555556E-01 7.00000000E-02
1.00000000E-01 1.05000000E+01 1.10000000E+00
%FLAG DIHEDRAL_PERIODICITY
%FORMAT(5E16.8)
1.00000000E+00 2.00000000E+00 2.00000000E+00 1.00000000E+00 3.00000000E+00
4.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00 2.00000000E+00
4.00000000E+00 2.00000000E+00 2.00000000E+00
%FLAG DIHEDRAL_PHASE
%FORMAT(5E16.8)
0.00000000E+00 3.14159400E+00 0.00000000E+00 0.00000000E+00 3.14159400E+00
3.14159400E+00 0.00000000E+00 3.14159400E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 3.14159400E+00 3.14159400E+00
%FLAG SOLTY
%FORMAT(5E16.8)
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
%FLAG LENNARD_JONES_ACOEF
%FORMAT(5E16.8)
9.44293233E+05 2.12601181E+03 1.39982777E-01 9.95480466E+05 2.56678134E+03
1.04308023E+06 2.01791425E+04 9.14716912E+00 2.27401052E+04 2.01823541E+02
8.96776989E+04 1.07193646E+02 9.71708117E+04 1.41077189E+03 7.51607703E+03
8.82619071E+05 2.27577561E+03 9.24822270E+05 2.01619733E+04 8.61541883E+04
8.19971662E+05 6.06829342E+05 1.02595236E+03 6.47841731E+05 1.12780457E+04
5.44261042E+04 5.74393458E+05 3.79876399E+05 6.20665997E+04 5.94667300E+01
6.78771368E+04 8.79040886E+02 4.98586848E+03 6.01816484E+04 3.69471530E+04
3.25969625E+03
%FLAG LENNARD_JONES_BCOEF
%FORMAT(5E16.8)
8.01323529E+02 2.09604198E+01 9.37598976E-02 7.36907417E+02 2.06278363E+01
6.75612247E+02 6.45756063E+01 7.57919667E-01 6.13981767E+01 3.56012899E+00
1.36131731E+02 2.59456373E+00 1.26919150E+02 9.41257003E+00 2.17257828E+01
6.53361429E+02 1.82891803E+01 5.99015525E+02 5.44372326E+01 1.12529845E+02
5.31102864E+02 6.77220874E+02 1.53505284E+01 6.26720080E+02 5.08951803E+01
1.11805549E+02 5.55666448E+02 5.64885984E+02 1.13252061E+02 1.93248820E+00
1.06076943E+02 7.42992380E+00 1.76949863E+01 9.40505980E+01 9.21192136E+01
1.43076527E+01
%FLAG BONDS_INC_HYDROGEN
%FORMAT(10I8)
18 21 3 18 24 3 18 27 3 12
15 4 0 3 7 0 6 7 0 9
7 48 51 3 48 54 3 48 57 3
42 45 10 36 39 11
%FLAG BONDS_WITHOUT_HYDROGEN
%FORMAT(10I8)
30 33 1 30 36 2 12 18 5 12
30 6 0 12 8 60 63 9 60 66
9 42 48 5 42 60 6 36 42 12
%FLAG ANGLES_INC_HYDROGEN
%FORMAT(10I8)
30 36 39 2 24 18 27 4 21 18
24 4 21 18 27 4 15 12 18 6
15 12 30 7 12 18 21 8 12 18
24 8 12 18 27 8 9 0 12 11
6 0 9 12 6 0 12 11 3 0
6 12 3 0 9 12 3 0 12 11
0 12 15 13 54 48 57 4 51 48
54 4 51 48 57 4 45 42 48 17
45 42 60 18 42 48 51 8 42 48
54 8 42 48 57 8 39 36 42 20
36 42 45 21
%FLAG ANGLES_WITHOUT_HYDROGEN
%FORMAT(10I8)
33 30 36 1 30 36 42 3 18 12
30 5 12 30 33 9 12 30 36 10
0 12 18 14 0 12 30 15 63 60
66 16 48 42 60 5 42 60 63 19
42 60 66 19 36 42 48 22 36 42
60 23
%FLAG DIHEDRALS_INC_HYDROGEN
%FORMAT(10I8)
33 30 36 39 1 33 30 -36 39 2
30 36 42 45 3 27 18 12 30 9
24 18 12 30 9 21 18 12 30 9
15 12 18 21 9 15 12 18 24 9
15 12 18 27 9 15 12 30 33 3
15 12 30 36 3 12 30 36 39 2
9 0 12 15 9 9 0 12 18 9
9 0 12 30 9 6 0 12 15 9
6 0 12 18 9 6 0 12 30 9
3 0 12 15 9 3 0 12 18 9
3 0 12 30 9 0 12 18 21 9
0 12 18 24 9 0 12 18 27 9
57 48 42 60 9 54 48 42 60 9
51 48 42 60 9 45 42 48 51 9
45 42 48 54 9 45 42 48 57 9
45 42 60 63 3 45 42 60 66 3
39 36 42 45 3 39 36 42 48 3
39 36 42 60 3 36 42 48 51 9
36 42 48 54 9 36 42 48 57 9
30 42 -36 -39 13
%FLAG DIHEDRALS_WITHOUT_HYDROGEN
%FORMAT(10I8)
33 30 36 42 2 30 36 42 48 4
30 36 -42 48 3 30 36 -42 48 5
30 36 -42 48 6 30 36 42 60 7
30 36 -42 60 8 18 12 30 33 3
18 12 30 36 10 18 12 -30 36 11
12 30 36 42 2 0 12 30 33 3
0 12 30 36 3 48 42 60 63 3
48 42 60 66 3 36 42 60 63 3
36 42 60 66 3 12 36 -30 -33 12
42 63 -60 -66 12
%FLAG EXCLUDED_ATOMS_LIST
%FORMAT(10I8)
2 3 4 5 6 7 8 9 10 11
12 13 3 4 5 6 7 11 4 5
6 7 11 5 6 7 11 6 7 8
9 10 11 12 13 14 15 7 8 9
10 11 12 13 8 9 10 11 12 13
9 10 11 10 11 11 12 13 14 15
16 17 21 13 14 15 14 15 16 17
18 19 20 21 22 23 15 16 17 21
16 17 18 19 20 21 22 23 17 18
19 20 21 22 23 18 19 20 21 22
23 19 20 21 20 21 21 22 23 23
0
%FLAG HBOND_ACOEF
%FORMAT(5E16.8)
%FLAG HBOND_BCOEF
%FORMAT(5E16.8)
%FLAG HBCUT
%FORMAT(5E16.8)
%FLAG AMBER_ATOM_TYPE
%FORMAT(20a4)
N3 H H H CT HP CT HC HC HC C O N H CT H1 CT HC HC HC
C O2 O2
%FLAG TREE_CHAIN_CLASSIFICATION
%FORMAT(20a4)
BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA
BLA BLA BLA
%FLAG JOIN_ARRAY
%FORMAT(10I8)
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0
%FLAG IROTAT
%FORMAT(10I8)
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0
%FLAG RADIUS_SET
%FORMAT(1a80)
modified Bondi radii (mbondi)
%FLAG RADII
%FORMAT(5E16.8)
1.55000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.70000000E+00
1.30000000E+00 1.70000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00
1.70000000E+00 1.50000000E+00 1.55000000E+00 1.30000000E+00 1.70000000E+00
1.30000000E+00 1.70000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00
1.70000000E+00 1.50000000E+00 1.50000000E+00
%FLAG SCREEN
%FORMAT(5E16.8)
7.90000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01
8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01
7.20000000E-01 8.50000000E-01 7.90000000E-01 8.50000000E-01 7.20000000E-01
8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01
7.20000000E-01 8.50000000E-01 8.50000000E-01