Hi,
I'm working on parametrization of Ruthenium-based chromophore for further all-atom MD.
I tried to make prep files by two ways, both failed:
1) I use g09 output file (see more below) to run antechamber:
antechamber -i chrom1_12.log -fi gout -o chrom1_12.prepin -fo prepi -c resp -at amber -s 2 -gv 1 -ge chrom1_12_respfile.gesp (fail at espgen stage)
The error message is:
espgen cannot deal with Gaussian 09 log file, please generate Gaussian 09 ESP file using iop(6/50=1) and rerun espgen
Error: cannot run "/Users/MariaM/amber12/bin/espgen -o ANTECHAMBER.ESP -i chrom1_12.log" in resp() of charge.c properly, exit
ANTECHAMBER.ESP file is empty
2) after doing step one I run:
2.1) respgen -i ANTECHAMBER_AC.AC -o chrom1_12.respin1 -f resp1 (success)
2.2) respgen -i ANTECHAMBER_AC.AC -o chrom1_12.respin2 -f resp2 (success)
2.3) resp -O -i chrom1_12.respin1 -o chrom1_12.respout1 -e ANTECHAMBER.ESP -t qout_stage1 (success)
2.4) resp -O -i chrom1_12.respin2 -o chrom1_12.respout2 -e ANTECHAMBER.ESP -q qout_stage1 -t qout_stage2 (success)
2.5) antechamber -i ANTECHAMBER_AC.AC -fi ac -o chrom1_12_resp.ac -fo ac -c rc -cf qout_stage2 (success, except for warning)
For atom[110]:Ru1, the best APS is not zero, bonds involved by this atom are frozen
2.6) prepgen -i chrom1_12_resp.ac -o chrom1_12.prepin -f int -rn BZ1
the file chrom1_12.prepin is created, but information about atom# > 58 is lost:
0 0 2
This is a remark line
molecule.res
BZ1 INT 0
CORRECT OMIT DU BEG
0.0000
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
4 O2 o M 3 2 1 1.540 111.208 -180.000 -0.486813
5 C20 c M 4 3 2 1.242 30.171 -64.174 0.434978
6 H6 h4 E 5 4 3 1.100 122.239 -24.438 0.056907
7 C17 c3 M 5 4 3 1.548 121.602 157.515 -0.027186
8 C19 c3 B 7 5 4 1.545 112.191 41.627 -0.083785
9 H5 hc E 8 7 5 1.095 109.037 -28.431 0.096385
10 H7 hc E 8 7 5 1.094 112.405 92.948 0.096385
11 H3 h1 E 7 5 4 1.098 107.838 166.763 0.060995
12 N7 n M 7 5 4 1.493 111.519 -73.624 -0.095454
13 C41 c B 12 7 5 1.379 118.989 -51.578 0.534850
14 O15 o E 13 12 7 1.262 119.178 1.195 -0.570831
15 C42 c3 3 13 12 7 1.518 117.858 -178.684 -0.197609
16 H41 hc E 15 13 12 1.091 108.368 -174.594 0.075016
17 H42 hc E 15 13 12 1.098 111.559 -54.574 0.075016
18 H43 hc E 15 13 12 1.098 111.088 66.131 0.075016
19 C16 c3 M 12 7 5 1.473 113.422 124.445 -0.135613
20 H1 h1 E 19 12 7 1.098 111.922 -98.958 0.108381
21 H2 h1 E 19 12 7 1.095 111.608 138.514 0.108381
22 C18 c3 M 19 12 7 1.550 102.210 18.424 -0.173188
23 H4 h1 E 22 19 12 1.096 110.023 85.429 0.136263
24 N1 na M 22 19 12 1.476 112.739 -155.655 0.518912
25 C1 cc S 24 22 19 1.376 129.296 -126.583 -0.448171
26 H8 h4 E 25 24 22 1.077 122.913 2.266 0.238542
27 N2 nc M 24 22 19 1.385 119.748 56.041 -0.419388
28 N3 nd M 27 24 22 1.337 106.237 177.922 -0.075864
29 C2 cd M 28 27 24 1.389 109.811 -0.077 0.257406
30 C3 c3 M 29 28 27 1.509 119.083 -179.773 -0.054636
31 H9 h1 E 30 29 28 1.098 111.739 -116.181 0.107542
32 H10 h1 E 30 29 28 1.097 111.835 124.263 0.107542
33 N4 n M 30 29 28 1.472 106.718 4.079 -0.165437
34 H11 hn E 33 30 29 1.020 113.483 -3.047 -0.008955
35 C4 c M 33 30 29 1.354 122.615 177.176 0.459953
36 O1 o E 35 33 30 1.263 124.046 1.137 -0.539587
37 C5 ca M 35 33 30 1.519 116.862 -178.562 0.040550
38 C7 ca B 37 35 33 1.411 125.530 3.043 -0.102250
39 C8 ca B 38 37 35 1.401 119.106 178.868 -0.109223
40 N5 nb E 39 38 37 1.361 122.679 0.271 0.075804
41 H14 h4 E 39 38 37 1.082 120.563 -179.666 0.140736
42 H13 ha E 38 37 35 1.085 122.668 -0.476 0.184645
43 C6 ca M 37 35 33 1.406 116.412 -177.811 -0.064493
44 H12 ha E 43 37 35 1.084 116.865 0.239 0.139061
45 C9 cp M 43 37 35 1.402 120.557 -179.203 0.033360
46 C10 cp M 45 43 37 1.478 123.834 179.859 0.021187
47 N6 nb M 46 45 43 1.377 115.229 -177.718 0.102653
48 C12 ca M 47 46 45 1.362 118.563 -179.831 -0.138256
49 H16 h4 E 48 47 46 1.083 116.634 -179.876 0.151130
50 C13 ca M 48 47 46 1.398 122.528 -0.237 -0.131907
51 H17 ha E 50 48 47 1.086 119.294 -179.750 0.171058
52 C14 ca M 50 48 47 1.415 120.085 0.301 0.164784
53 C15 c3 3 52 50 48 1.510 121.507 178.823 -0.330501
54 H18 hc E 53 52 50 1.095 111.465 36.533 0.132278
55 H19 hc E 53 52 50 1.095 111.863 157.969 0.132278
56 H20 hc E 53 52 50 1.098 110.414 -82.439 0.132278
57 C11 ca M 52 50 48 1.411 116.877 -0.281 -0.155728
58 H15 ha E 57 52 50 1.084 119.277 -179.909 0.173412
59 X 1 0 1 14.095 nan 0.000 0.000000
60 X 1 0 1 14.095 nan 0.000 0.000000
61 X 1 0 1 14.095 nan 0.000 0.000000
62 X 1 0 1 14.095 nan 0.000 0.000000
63 X 1 0 1 14.095 nan 0.000 0.000000
64 X 1 0 1 14.095 nan 0.000 0.000000
65 X 1 0 1 14.095 nan 0.000 0.000000
66 X 1 0 1 14.095 nan 0.000 0.000000
67 X 1 0 1 14.095 nan 0.000 0.000000
68 X 1 0 1 14.095 nan 0.000 0.000000
69 X 1 0 1 14.095 nan 0.000 0.000000
70 X 1 0 1 14.095 nan 0.000 0.000000
71 X 1 0 1 14.095 nan 0.000 0.000000
72 X 1 0 1 14.095 nan 0.000 0.000000
73 X 1 0 1 14.095 nan 0.000 0.000000
74 X 1 0 1 14.095 nan 0.000 0.000000
75 X 1 0 1 14.095 nan 0.000 0.000000
76 X 1 0 1 14.095 nan 0.000 0.000000
77 X 1 0 1 14.095 nan 0.000 0.000000
78 X 1 0 1 14.095 nan 0.000 0.000000
79 X 1 0 1 14.095 nan 0.000 0.000000
80 X 1 0 1 14.095 nan 0.000 0.000000
81 X 1 0 1 14.095 nan 0.000 0.000000
82 X 1 0 1 14.095 nan 0.000 0.000000
83 X 1 0 1 14.095 nan 0.000 0.000000
84 X 1 0 1 14.095 nan 0.000 0.000000
85 X 1 0 1 14.095 nan 0.000 0.000000
86 X 1 0 1 14.095 nan 0.000 0.000000
87 X 1 0 1 14.095 nan 0.000 0.000000
88 X 1 0 1 14.095 nan 0.000 0.000000
89 X 1 0 1 14.095 nan 0.000 0.000000
90 X 1 0 1 14.095 nan 0.000 0.000000
91 X 1 0 1 14.095 nan 0.000 0.000000
92 X 1 0 1 14.095 nan 0.000 0.000000
93 X 1 0 1 14.095 nan 0.000 0.000000
94 X 1 0 1 14.095 nan 0.000 0.000000
95 X 1 0 1 14.095 nan 0.000 0.000000
96 X 1 0 1 14.095 nan 0.000 0.000000
97 X 1 0 1 14.095 nan 0.000 0.000000
98 X 1 0 1 14.095 nan 0.000 0.000000
99 X 1 0 1 14.095 nan 0.000 0.000000
100 X 1 0 1 14.095 nan 0.000 0.000000
101 X 1 0 1 14.095 nan 0.000 0.000000
102 X 1 0 1 14.095 nan 0.000 0.000000
103 X 1 0 1 14.095 nan 0.000 0.000000
104 X 1 0 1 14.095 nan 0.000 0.000000
105 X 1 0 1 14.095 nan 0.000 0.000000
106 X 1 0 1 14.095 nan 0.000 0.000000
107 X 1 0 1 14.095 nan 0.000 0.000000
108 X 1 0 1 14.095 nan 0.000 0.000000
109 X 1 0 1 14.095 nan 0.000 0.000000
110 X 1 0 1 14.095 nan 0.000 0.000000
111 X 1 0 1 14.095 nan 0.000 0.000000
112 X 1 0 1 14.095 nan 0.000 0.000000
113 X 1 0 1 14.095 nan 0.000 0.000000
114 X 1 0 1 14.095 nan 0.000 0.000000
115 X 1 0 1 14.095 nan 0.000 0.000000
116 X 1 0 1 14.095 nan 0.000 0.000000
117 X 1 0 1 14.095 nan 0.000 0.000000
118 X 1 0 1 14.095 nan 0.000 0.000000
119 X 1 0 1 14.095 nan 0.000 0.000000
LOOP
C18 C19
C2 C1
C9 N5
C11 C10
IMPROPER
C17 H6 C20 O2
C41 C16 N7 C17
C42 N7 C41 O15
C18 C1 N1 N2
C2 H8 C1 N1
C3 C1 C2 N3
C3 C4 N4 H11
C5 N4 C4 O1
C4 C7 C5 C6
C5 C8 C7 H13
C7 H14 C8 N5
C5 C9 C6 H12
C6 C10 C9 N5
C11 C9 C10 N6
C13 H16 C12 N6
C12 C14 C13 H17
C15 C13 C14 C11
C14 C10 C11 H15
DONE
STOP
Additional info:
The chromophore consists of 116 atoms. I ran DFT to optimize structure and get esp charges on Gaussian 09 with the input line:
# opt b3lyp/lanl2dz geom=connectivity pop=(mk,readradii) iop(6/50=1)
... and last two lines from *.com:
44 2.0
44 2.0
Can anything be done to make prepgen process large molecules like this?
With best regards, Maria Minakova.
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Received on Thu Jun 28 2012 - 14:30:03 PDT
