Holle all:
After using amber16 for classical dynamics simulation, I directly used the generated prmtop file and rst file for QM/MM MD simulation with gaussian09. But I found the Fe which in the QM region, is written as F (and the atomic number is written as 9) in gau_job.log and gau_job.Inp. This is obviously abnormal. I don't know how to solve this problems. Here are some related documents.
Part of gau_job.Inp. The QM region should have no F element
%chk=gau_job.chk
%NProcShared=8
%mem=1GB
#P B3LYP/6-31G(d,p) SCF=(Conver=8) NoSymm Force Charge Prop=(Field,Read)
Gaussian run using SANDER external interface.
0 2
C 1.0982654285351443 3.7232869864444029 5.1022333415211172
O 1.4930444377349248 4.1570944415518198 3.9744397773796787
O 1.0217442724739685 4.4852583684407827 6.1167632507231664
C -7.4681119776187739 -0.6378082092000998 -4.1492011915722493
S -7.1317202447189540 -1.0420427213645969 -2.4212457451589522
N -4.9379352736791073 -1.8191017894430841 -0.4685006237014448
C -5.5369595656741364 -1.7778759497654208 0.8108889105857919
C -4.3767468063921315 -3.0875692745790762 -0.4401108996562400
C -5.3739851571970876 -2.9825506048152057 1.5610759853124918
C -4.6530541212491672 -3.8697605488819415 0.7159023060844411
C -3.7072892562488535 -3.5229516307315580 -1.6339637750662488
H -3.1989066766238405 -4.4852583684407827 -1.5960968880664801
C -3.5970265835000932 -2.8521345307439430 -2.8851426317525433
N -3.9460015590682338 -1.5331328825375057 -3.1369309325698782
C -3.4765335755551932 -1.2476494776844367 -4.3948899532961869
C -2.9149152162206895 -2.4211069957475537 -5.0261905440545664
C -2.9774580760056093 -3.4173789731595967 -4.0382936603998161
C -3.7699816837627282 0.0005410218958642 -5.0660879362932922
H -3.4883651945635186 0.0524499489148937 -6.1167632507231611
C -4.5348303999196116 1.0780895041804766 -4.4936592385400047
C -5.0175065922305873 2.1561312205212753 -5.3188481695614467
C -5.6193015132005240 2.3431008530202195 -3.1213486373388686
N -4.9247848349655978 1.1603876432086262 -3.1752053648301017
C -5.5993101249329458 3.0859894485995376 -4.3411311357446607
C -6.3313436002082693 2.8342549218455395 -1.9071001061341342
H -6.9042863706798325 3.7484874440132376 -2.0548775574098705
C -6.5140319910513735 2.1420561612991125 -0.6654620906501343
C -7.3053530315774804 2.5940700062431228 0.4476393453265039
N -5.7750538554424065 0.9747012139259493 -0.3945147015237893
C -6.2966374796372024 0.6413889759996485 0.8569857348973464
C -6.0891620406958440 -0.6453150398161506 1.3644169074196524
H -6.6227552651935016 -0.7219103145968413 2.3106370492841464
F -4.8273645562277121 -0.2469488806248424 -1.7449897911021102
C -7.1177226768685431 1.5992875309134691 1.4341117783203323
O -3.4014699565678210 0.3260308565433452 -1.1717098730591324
N 2.1321886806073009 1.8139617415231784 1.8033637762073338
C 3.3376912472247695 0.1571616681448562 0.9449380633824447
C 2.1553648015121154 0.3974889790734652 0.0751665530963912
C 3.1807479522019348 1.0151857667101669 2.0831824504492253
C 1.6059464908391674 1.5604233035233748 0.5768459644444056
C 4.5209580766785971 -0.6504981913026010 0.9381473976447302
C 1.5530492326952881 -0.3176480473236170 -1.0145050066247876
C 5.2357311753963325 -0.8980701956036546 2.1690071413144025
C 0.5241503029873884 0.4664978744732561 -1.6207794108787998
C 3.8899007189517159 0.8599732995942744 3.3136171747678702
C 0.5766880514577241 2.2982960728493360 0.0635463270126522
C 4.8534245119985835 -0.2030823141028759 3.3697553315166675
C 0.0473663071924138 1.6961050322685767 -1.0906431644999515
C 4.8707503778984469 -1.2866538627309418 -0.2328621044299908
C 1.8445817781648530 -1.6369675542931310 -1.4490871147868665
C 6.3009085612745119 -1.8828496594765896 2.0603281260248352
C -0.1088727826478984 -0.0870803532008789 -2.7414914942725477
C 5.9014642748770800 -2.2929872253941244 -0.2653328394984769
C 1.2417284734084872 -2.1688114914195995 -2.5599457262733369
C 6.6267172716415823 -2.5411293899278431 0.8717025932198297
C 0.2429494122794312 -1.4049635043973885 -3.1815065450155124
H 1.5468889773733012 2.2102302717753539 2.5248183824617598
H 3.5142747093838143 1.4531227050288233 4.1421549734344154
H 0.1916021835424660 3.1513287800953362 0.6144002782452134
H 5.4244465379800255 -0.4038045538173096 4.2714431151847192
H -0.8100064550873666 2.1545074831166744 -1.5745596238097261
H 4.3899863358061362 -1.0905739504482972 -1.1867041269177356
H 2.5645819378354004 -2.1969814100982874 -0.8596973865701364
H 6.8782893972847887 -2.1221529804152248 2.9484506974175453
H -0.8563380938721591 0.5192330476018369 -3.2445577611892098
H 6.1542043136569706 -2.8848271467838176 -1.1401150868800050
H 1.3883828229072479 -3.1668364831156124 -2.9622324621070071
H 7.4681119776187765 -3.2277382321909398 0.8763207055006426
H -0.2399194666976410 -1.9385029091931902 -3.9948756820104054
H 0.9250114959810413 2.6482629517424630 5.1512884092277273
H -7.3444623563452325 -1.4331157214050760 -4.8842499873601488
H -7.5972272944074426 1.4670323720395497 2.4040003774440191
H -4.3087994402118852 -4.8966268506497626 0.8389239012521091
H -7.9041471407827615 3.5005273990461681 0.5364121441657892
H -5.7910832503397600 -3.1487278828276315 2.5543102441704555
H -2.5223552894323293 -4.4068516922376242 -4.0821706686566408
H -6.0850845466344339 4.0220804010016957 -4.6165525220809558
H -4.8190879853346722 2.4102233932133874 -6.3600816804580589
H -2.5440717324927995 -2.5502070947668951 -6.0430033463981232
Part of the log file (Fe number 33)
Leave Link 103 at Wed Jun 15 12:20:46 2022, MaxMem= 134217728 cpu: 0.1
(Enter /home/zqc-gpu03/fs/g09/l202.exe)
Symmetry turned off by external request.
Stoichiometry C42H27FN5O3S(2)
Framework group C1[X(C42H27FN5O3S)]
Deg. of freedom 231
Full point group C1 NOp 1
Input orientation:
---------------------------------------------------------------------
Center Atomic Atomic Coordinates (Angstroms)
Number Number Type X Y Z
---------------------------------------------------------------------
1 6 0 1.098265 3.723287 5.102233
2 8 0 1.493044 4.157094 3.974440
3 8 0 1.021744 4.485258 6.116763
4 6 0 -7.468112 -0.637808 -4.149201
5 16 0 -7.131720 -1.042043 -2.421246
6 7 0 -4.937935 -1.819102 -0.468501
7 6 0 -5.536960 -1.777876 0.810889
8 6 0 -4.376747 -3.087569 -0.440111
9 6 0 -5.373985 -2.982551 1.561076
10 6 0 -4.653054 -3.869761 0.715902
11 6 0 -3.707289 -3.522952 -1.633964
12 1 0 -3.198907 -4.485258 -1.596097
13 6 0 -3.597027 -2.852135 -2.885143
14 7 0 -3.946002 -1.533133 -3.136931
15 6 0 -3.476534 -1.247649 -4.394890
16 6 0 -2.914915 -2.421107 -5.026191
17 6 0 -2.977458 -3.417379 -4.038294
18 6 0 -3.769982 0.000541 -5.066088
19 1 0 -3.488365 0.052450 -6.116763
20 6 0 -4.534830 1.078090 -4.493659
21 6 0 -5.017507 2.156131 -5.318848
22 6 0 -5.619302 2.343101 -3.121349
23 7 0 -4.924785 1.160388 -3.175205
24 6 0 -5.599310 3.085989 -4.341131
25 6 0 -6.331344 2.834255 -1.907100
26 1 0 -6.904286 3.748487 -2.054878
27 6 0 -6.514032 2.142056 -0.665462
28 6 0 -7.305353 2.594070 0.447639
29 7 0 -5.775054 0.974701 -0.394515
30 6 0 -6.296637 0.641389 0.856986
31 6 0 -6.089162 -0.645315 1.364417
32 1 0 -6.622755 -0.721910 2.310637
33 9 0 -4.827365 -0.246949 -1.744990
34 6 0 -7.117723 1.599288 1.434112
35 8 0 -3.401470 0.326031 -1.171710
36 7 0 2.132189 1.813962 1.803364
37 6 0 3.337691 0.157162 0.944938
38 6 0 2.155365 0.397489 0.075167
39 6 0 3.180748 1.015186 2.083182
40 6 0 1.605946 1.560423 0.576846
41 6 0 4.520958 -0.650498 0.938147
42 6 0 1.553049 -0.317648 -1.014505
43 6 0 5.235731 -0.898070 2.169007
44 6 0 0.524150 0.466498 -1.620779
45 6 0 3.889901 0.859973 3.313617
46 6 0 0.576688 2.298296 0.063546
47 6 0 4.853425 -0.203082 3.369755
48 6 0 0.047366 1.696105 -1.090643
49 6 0 4.870750 -1.286654 -0.232862
50 6 0 1.844582 -1.636968 -1.449087
51 6 0 6.300909 -1.882850 2.060328
52 6 0 -0.108873 -0.087080 -2.741491
53 6 0 5.901464 -2.292987 -0.265333
54 6 0 1.241728 -2.168811 -2.559946
55 6 0 6.626717 -2.541129 0.871703
56 6 0 0.242949 -1.404964 -3.181507
57 1 0 1.546889 2.210230 2.524818
58 1 0 3.514275 1.453123 4.142155
59 1 0 0.191602 3.151329 0.614400
60 1 0 5.424447 -0.403805 4.271443
61 1 0 -0.810006 2.154507 -1.574560
62 1 0 4.389986 -1.090574 -1.186704
63 1 0 2.564582 -2.196981 -0.859697
64 1 0 6.878289 -2.122153 2.948451
65 1 0 -0.856338 0.519233 -3.244558
66 1 0 6.154204 -2.884827 -1.140115
67 1 0 1.388383 -3.166836 -2.962232
68 1 0 7.468112 -3.227738 0.876321
69 1 0 -0.239919 -1.938503 -3.994876
70 1 0 0.925011 2.648263 5.151288
71 1 0 -7.344462 -1.433116 -4.884250
72 1 0 -7.597227 1.467032 2.404000
73 1 0 -4.308799 -4.896627 0.838924
74 1 0 -7.904147 3.500527 0.536412
75 1 0 -5.791083 -3.148728 2.554310
76 1 0 -2.522355 -4.406852 -4.082171
77 1 0 -6.085085 4.022080 -4.616553
78 1 0 -4.819088 2.410223 -6.360082
79 1 0 -2.544072 -2.550207 -6.043003
Part of pdb file.
HETATM 7649 CAA HEM A 479 -23.512 44.321 -31.020 1.00 0.00 C
HETATM 7650 CAB HEM A 479 -19.795 40.572 -39.156 1.00 0.00 C
HETATM 7651 CAC HEM A 479 -13.561 42.678 -34.801 1.00 0.00 C
HETATM 7652 CAD HEM A 479 -18.420 45.022 -29.117 1.00 0.00 C
HETATM 7653 NA HEM A 479 -20.940 43.393 -33.589 1.00 0.00 N
HETATM 7654 CBA HEM A 479 -23.849 45.800 -30.853 1.00 0.00 C
HETATM 7655 CBB HEM A 479 -20.615 40.190 -40.094 1.00 0.00 C
HETATM 7656 CBC HEM A 479 -12.546 42.430 -35.589 1.00 0.00 C
HETATM 7657 CBD HEM A 479 -18.676 46.539 -29.097 1.00 0.00 C
HETATM 7658 NB HEM A 479 -19.867 42.203 -35.955 1.00 0.00 N
HETATM 7659 CGA HEM A 479 -24.554 46.024 -29.533 1.00 0.00 C
HETATM 7660 CGD HEM A 479 -19.039 47.007 -27.702 1.00 0.00 C
HETATM 7661 ND HEM A 479 -18.372 43.792 -32.688 1.00 0.00 N
HETATM 7662 CHA HEM A 479 -20.394 44.274 -31.397 1.00 0.00 C
HETATM 7663 CHB HEM A 479 -22.230 42.520 -35.388 1.00 0.00 C
HETATM 7664 CHC HEM A 479 -17.815 41.602 -37.097 1.00 0.00 C
HETATM 7665 CHD HEM A 479 -15.947 43.439 -33.060 1.00 0.00 C
HETATM 7666 CMA HEM A 479 -24.654 43.196 -33.652 1.00 0.00 C
HETATM 7667 CMB HEM A 479 -22.714 41.176 -38.057 1.00 0.00 C
HETATM 7668 CMC HEM A 479 -14.734 41.465 -37.540 1.00 0.00 C
HETATM 7669 CMD HEM A 479 -15.602 44.497 -30.185 1.00 0.00 C
HETATM 7670 C1A HEM A 479 -21.278 43.852 -32.344 1.00 0.00 C
HETATM 7671 C1B HEM A 479 -21.171 42.092 -36.176 1.00 0.00 C
HETATM 7672 C1C HEM A 479 -16.888 42.053 -36.184 1.00 0.00 C
HETATM 7673 C1D HEM A 479 -17.055 43.760 -32.301 1.00 0.00 C
HETATM 7674 O1 HEM A 479 -18.926 41.543 -33.664 1.00 0.00 O
HETATM 7675 O1A HEM A 479 -25.278 47.056 -29.447 1.00 0.00 O
HETATM 7676 O1D HEM A 479 -19.048 48.250 -27.341 1.00 0.00 O
HETATM 7677 C2A HEM A 479 -22.682 43.910 -32.216 1.00 0.00 C
HETATM 7678 C2B HEM A 479 -21.402 41.461 -37.421 1.00 0.00 C
HETATM 7679 C2C HEM A 479 -15.499 41.959 -36.321 1.00 0.00 C
HETATM 7680 C2D HEM A 479 -16.879 44.243 -30.958 1.00 0.00 C
HETATM 7681 O2A HEM A 479 -24.428 45.252 -28.496 1.00 0.00 O1-
HETATM 7682 O2D HEM A 479 -19.354 46.089 -26.890 1.00 0.00 O1-
HETATM 7683 C3A HEM A 479 -23.182 43.398 -33.341 1.00 0.00 C
HETATM 7684 C3B HEM A 479 -20.170 41.194 -37.907 1.00 0.00 C
HETATM 7685 C3C HEM A 479 -14.977 42.491 -35.160 1.00 0.00 C
HETATM 7686 C3D HEM A 479 -18.105 44.501 -30.506 1.00 0.00 C
HETATM 7687 C4A HEM A 479 -22.101 43.096 -34.182 1.00 0.00 C
HETATM 7688 C4B HEM A 479 -19.190 41.655 -36.904 1.00 0.00 C
HETATM 7689 C4C HEM A 479 -16.059 42.884 -34.328 1.00 0.00 C
HETATM 7690 C4D HEM A 479 -19.030 44.164 -31.583 1.00 0.00 C
HETATM 7691 NC HEM A 479 -17.199 42.610 -35.002 1.00 0.00 N
HETATM 7692 FE HEM A 479 -19.100 43.059 -34.290 1.00 0.00 FE4+
Can someone help me with this please.
Best
Fengshi
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Received on Thu Aug 04 2022 - 13:32:16 PDT
