Dear amber users,
I was trying to go through the tutorial () using amber tools 17. My amber tools 17 was installed through anaconda (python 3.6). The "workflow" I got from running "antechamber -i sustiva_new.pdb -fi pdb -o sustiva.mol2 -fo mol2 -c bcc -s 2" was:
1. Bondtype
2. Atomtype
3. Sqm (it was mopac in the tutorial. Someone said mopac was used in older versions)
4. Am1bcc
5. Atomtype
I compared the input and output geometry from sqm (step3) and input structure for am1bcc (step4) that was contained in "ANTECHAMBER_AM1BCC_PRE.AC". Also the mulliken charges in sqm.out(step3) and the charges "ANTECHAMBER_AM1BCC_PRE.AC"(step4)
a. This input geometry for am1bcc wasn't the output from sqm, but the input for sqm. This make no sense to me. Although in the manual, it did say, you could use "maxcyc=0" in sqm to let it direct output geometry without any changes, so as to check the sensitivity of geometry dependence of charge assignment on different geometry, there is no such keyword used in "sqm.in". I suppose am1bcc should use the output from sqm.out
b. The mulliken charges in the sqm.out only have value for "step 1". Do we used this as the final result? But it is not exactly the same as in "ANTECHAMBER_AM1BCC_PRE.AC". Most of them are the same but there is one or two are different. I suppose the charge in "ANTECHAMBER_AM1BCC_PRE.AC" should come from the mulliken charges in sqm.out. But the fact that sqm.out only contains mulliken charge for "step 1" makes me confused.
c. In the sqm.in the keyword are "AM1, grms_tol=0.005 ... etc". there is a python script in "/opt/anaconda/lib/python3.6/site-packages/pymsmt/mol/sqmio.py" that was installed by ambertools. In this script, the section "write sqm input file", it reads "print(" qm_theory='PM6', grms_tol=0.0002,", file=sqm_scf)". So my question is, why these two are different? Is this sqmio.py not intended for antechamber workflow?
Thank you very much for help!!
Best,
Shuo
I post the related files here:
"sqm.in":
Run semi-empirical minimization
&qmmm
qm_theory='AM1', grms_tol=0.0005,
scfconv=1.d-10, ndiis_attempts=700, qmcharge=0,
/
17 CL -4.6850 -32.7250 25.2220
9 F1 -0.7550 -36.6320 25.6970
9 F2 1.0780 -37.0430 24.6720
9 F3 -0.7840 -37.1770 23.6260
8 O1 1.5240 -34.9340 20.9100
8 O2 0.9890 -34.8800 23.0580
7 N -0.6810 -34.9710 21.4340
6 C1 -1.6620 -34.4140 22.3130
6 C2 -2.9150 -33.9470 21.8430
6 C3 -3.8380 -33.4230 22.7710
6 C4 -3.5330 -33.3730 24.1190
6 C5 -2.3100 -33.8290 24.5930
6 C6 -1.3860 -34.3780 23.6810
6 C7 -0.0020 -34.9570 24.1440
6 C8 0.5520 -34.2360 25.3150
6 C9 0.9850 -33.6570 26.2410
6 C10 1.6050 -32.8020 27.5860
6 C11 2.8080 -33.0830 27.6390
6 C12 2.4040 -31.9800 27.1230
6 C13 -0.1210 -36.4720 24.5390
6 C14 0.6650 -34.9320 21.7250
1 H122 2.4640 -31.8200 26.1680
1 H121 2.5630 -31.1310 27.5640
1 H112 3.2840 -33.0980 28.4840
1 H111 3.1850 -33.7870 27.0890
1 H101 0.8810 -32.7660 28.2300
1 HN -0.9390 -35.3410 20.7020
1 H5 -2.0950 -33.7710 25.5370
1 H3 -4.6960 -33.0940 22.4610
1 H2 -3.1340 -33.9870 20.8990
"Sqm.out" result part:
RESULTS
--------------------------------------------------------------------------------
iter sqm energy rms gradient
---- ------------------- -----------------------
xmin 10 -119.8014 kcal/mol 0.7720 kcal/(mol*A)
xmin 20 -120.3109 kcal/mol 0.4028 kcal/(mol*A)
xmin 30 -120.4267 kcal/mol 0.1929 kcal/(mol*A)
xmin 40 -120.4375 kcal/mol 0.1871 kcal/(mol*A)
xmin 50 -120.4398 kcal/mol 0.0682 kcal/(mol*A)
xmin 60 -120.4417 kcal/mol 0.0139 kcal/(mol*A)
xmin 70 -120.4495 kcal/mol 0.0254 kcal/(mol*A)
xmin 80 -120.4660 kcal/mol 0.1567 kcal/(mol*A)
xmin 90 -120.4745 kcal/mol 0.0637 kcal/(mol*A)
xmin 100 -120.4813 kcal/mol 0.0369 kcal/(mol*A)
xmin 110 -120.4898 kcal/mol 0.0406 kcal/(mol*A)
xmin 120 -120.4936 kcal/mol 0.1119 kcal/(mol*A)
xmin 130 -120.4994 kcal/mol 0.1293 kcal/(mol*A)
xmin 140 -120.5023 kcal/mol 0.0218 kcal/(mol*A)
xmin 150 -120.5028 kcal/mol 0.0077 kcal/(mol*A)
xmin 160 -120.5032 kcal/mol 0.0177 kcal/(mol*A)
xmin 170 -120.5034 kcal/mol 0.0042 kcal/(mol*A)
xmin 180 -120.5035 kcal/mol 0.0071 kcal/(mol*A)
xmin 190 -120.5036 kcal/mol 0.0181 kcal/(mol*A)
xmin 200 -120.5037 kcal/mol 0.0228 kcal/(mol*A)
xmin 210 -120.5037 kcal/mol 0.0044 kcal/(mol*A)
xmin 220 -120.5037 kcal/mol 0.0032 kcal/(mol*A)
xmin 230 -120.5037 kcal/mol 0.0073 kcal/(mol*A)
xmin 240 -120.5038 kcal/mol 0.0051 kcal/(mol*A)
xmin 250 -120.5038 kcal/mol 0.0027 kcal/(mol*A)
xmin 260 -120.5038 kcal/mol 0.0009 kcal/(mol*A)
xmin 270 -120.5038 kcal/mol 0.0006 kcal/(mol*A)
... geometry converged !
Final MO eigenvalues (eV):
-52.0466 -48.8096 -48.7111 -42.3075 -39.9582 -39.3514 -38.4377 -38.0558
-36.2649 -34.8411 -32.6747 -30.9911 -29.4946 -25.9619 -25.4726 -24.7143
-24.1167 -23.6194 -21.5542 -20.9676 -20.1840 -19.6855 -19.3416 -19.1758
-18.4884 -17.7235 -17.2548 -16.8762 -16.5897 -16.4726 -16.0900 -15.6573
-15.4088 -15.3225 -15.1878 -14.9764 -14.7663 -14.4739 -14.4714 -14.2670
-13.9467 -13.7868 -13.6433 -13.3456 -13.1764 -12.6484 -12.6267 -12.3403
-12.2106 -11.9300 -11.8069 -11.1302 -10.7483 -10.6363 -9.4401 -0.7346
-0.5086 0.2988 0.4796 0.9161 0.9799 1.1108 1.3083 1.7831
1.9120 2.4117 2.5237 2.8372 2.9219 3.2256 3.2612 3.3181
3.3710 3.3965 3.4413 3.6001 3.6650 3.7428 3.8594 4.0847
4.1229 4.2165 4.2997 4.5137 4.5208 4.5639 4.6300 4.6715
4.8455 4.8971 5.8232 6.0612 6.3807
Heat of formation = -120.50380200 kcal/mol ( -5.22543697 eV)
Total SCF energy = -105867.28362924 kcal/mol ( -4590.74990804 eV)
Electronic energy = -613791.70441172 kcal/mol ( -26616.00556835 eV)
Core-core repulsion = 507924.42078248 kcal/mol ( 22025.25566031 eV)
Atomic Charges for Step 1 :
Atom Element Mulliken Charge
1 Cl 0.004
2 F -0.160
3 F -0.143
4 F -0.156
5 O -0.307
6 O -0.217
7 N -0.328
8 C 0.115
9 C -0.172
10 C -0.068
11 C -0.096
12 C -0.053
13 C -0.168
14 C 0.262
15 C -0.231
16 C -0.013
17 C -0.095
18 C -0.187
19 C -0.186
20 C 0.413
21 C 0.411
22 H 0.126
23 H 0.117
24 H 0.117
25 H 0.125
26 H 0.143
27 H 0.270
28 H 0.170
29 H 0.156
30 H 0.149
Total Mulliken Charge = -0.000
X Y Z TOTAL
QM DIPOLE -2.719 4.049 0.483 4.901
Final Structure
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 Cl -4.9215 -33.7218 25.3840
QMMM: 2 2 F -0.8716 -36.5938 25.8774
QMMM: 3 3 F 1.0661 -37.0435 25.0065
QMMM: 4 4 F -0.7433 -37.3874 23.8571
QMMM: 5 5 O 1.5980 -34.9059 21.0071
QMMM: 6 6 O 0.9042 -35.1774 23.0600
QMMM: 7 7 N -0.6188 -34.3059 21.4070
QMMM: 8 8 C -1.6495 -34.1838 22.3361
QMMM: 9 9 C -2.9248 -33.7131 21.9492
QMMM: 10 10 C -3.9317 -33.5766 22.8939
QMMM: 11 11 C -3.6868 -33.9014 24.2338
QMMM: 12 12 C -2.4343 -34.3705 24.6297
QMMM: 13 13 C -1.4137 -34.5252 23.6882
QMMM: 14 14 C -0.0592 -35.0107 24.1188
QMMM: 15 15 C 0.5188 -34.1325 25.1085
QMMM: 16 16 C 1.0145 -33.3932 25.9091
QMMM: 17 17 C 1.5724 -32.5134 26.8654
QMMM: 18 18 C 2.4955 -33.0478 27.9395
QMMM: 19 19 C 3.0545 -32.2069 26.8360
QMMM: 20 20 C -0.1534 -36.4996 24.7157
QMMM: 21 21 C 0.6342 -34.7794 21.7693
QMMM: 22 22 H 3.6837 -32.6835 26.0628
QMMM: 23 23 H 3.3729 -31.1709 27.0497
QMMM: 24 24 H 2.4075 -32.6232 28.9555
QMMM: 25 25 H 2.7234 -34.1286 27.9597
QMMM: 26 26 H 0.8768 -31.6896 27.1408
QMMM: 27 27 H -0.7728 -34.0633 20.4544
QMMM: 28 28 H -2.2412 -34.6289 25.6856
QMMM: 29 29 H -4.9241 -33.2100 22.5853
QMMM: 30 30 H -3.1249 -33.4520 20.8987
--------- Calculation Completed ----------
Input for am1bcc "ANTECHAMBER_AM1BCC_PRE.AC"
CHARGE 0.00 ( 0 )
Formula: H9 C14 N1 O2 F3 Cl1
ATOM 1 CL SUS 999 -4.685 -32.725 25.222 0.004000 cl
ATOM 2 F1 SUS 999 -0.755 -36.632 25.697 -0.153000 f
ATOM 3 F2 SUS 999 1.078 -37.043 24.672 -0.153000 f
ATOM 4 F3 SUS 999 -0.784 -37.177 23.626 -0.153000 f
ATOM 5 O1 SUS 999 1.524 -34.934 20.910 -0.307000 o
ATOM 6 O2 SUS 999 0.989 -34.880 23.058 -0.217000 os
ATOM 7 N SUS 999 -0.681 -34.971 21.434 -0.328000 n
ATOM 8 C1 SUS 999 -1.662 -34.414 22.313 0.115000 ca
ATOM 9 C2 SUS 999 -2.915 -33.947 21.843 -0.172000 ca
ATOM 10 C3 SUS 999 -3.838 -33.423 22.771 -0.068000 ca
ATOM 11 C4 SUS 999 -3.533 -33.373 24.119 -0.096000 ca
ATOM 12 C5 SUS 999 -2.310 -33.829 24.593 -0.053000 ca
ATOM 13 C6 SUS 999 -1.386 -34.378 23.681 -0.168000 ca
ATOM 14 C7 SUS 999 -0.002 -34.957 24.144 0.262000 c3
ATOM 15 C8 SUS 999 0.552 -34.236 25.315 -0.231000 c1
ATOM 16 C9 SUS 999 0.985 -33.657 26.241 -0.013000 c1
ATOM 17 C10 SUS 999 1.605 -32.802 27.586 -0.095000 cx
ATOM 18 C11 SUS 999 2.808 -33.083 27.639 -0.186500 cx
ATOM 19 C12 SUS 999 2.404 -31.980 27.123 -0.186500 cx
ATOM 20 C13 SUS 999 -0.121 -36.472 24.539 0.413000 c3
ATOM 21 C14 SUS 999 0.665 -34.932 21.725 0.411000 c
ATOM 22 H122SUS 999 2.464 -31.820 26.168 0.121250 hc
ATOM 23 H121SUS 999 2.563 -31.131 27.564 0.121250 hc
ATOM 24 H112SUS 999 3.284 -33.098 28.484 0.121250 hc
ATOM 25 H111SUS 999 3.185 -33.787 27.089 0.121250 hc
ATOM 26 H101SUS 999 0.881 -32.766 28.230 0.143000 hc
ATOM 27 HN SUS 999 -0.939 -35.341 20.702 0.270000 hn
ATOM 28 H5 SUS 999 -2.095 -33.771 25.537 0.170000 ha
ATOM 29 H3 SUS 999 -4.696 -33.094 22.461 0.156000 ha
ATOM 30 H2 SUS 999 -3.134 -33.987 20.899 0.149000 ha
BOND 1 1 11 1 CL C4
BOND 2 2 20 1 F1 C13
BOND 3 3 20 1 F2 C13
BOND 4 4 20 1 F3 C13
BOND 5 5 21 2 O1 C14
BOND 6 6 14 1 O2 C7
BOND 7 6 21 1 O2 C14
BOND 8 7 8 1 N C1
BOND 9 7 21 1 N C14
BOND 10 7 27 1 N HN
BOND 11 8 9 7 C1 C2
BOND 12 8 13 8 C1 C6
BOND 13 9 10 8 C2 C3
BOND 14 9 30 1 C2 H2
BOND 15 10 11 7 C3 C4
BOND 16 10 29 1 C3 H3
BOND 17 11 12 8 C4 C5
BOND 18 12 13 7 C5 C6
BOND 19 12 28 1 C5 H5
BOND 20 13 14 1 C6 C7
BOND 21 14 15 1 C7 C8
BOND 22 14 20 1 C7 C13
BOND 23 15 16 3 C8 C9
BOND 24 16 17 1 C9 C10
BOND 25 17 18 1 C10 C11
BOND 26 17 19 1 C10 C12
BOND 27 17 26 1 C10 H101
BOND 28 18 19 1 C11 C12
BOND 29 18 24 1 C11 H112
BOND 30 18 25 1 C11 H111
BOND 31 19 22 1 C12 H122
BOND 32 19 23 1 C12 H121
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Received on Thu Mar 22 2018 - 17:30:02 PDT
