Dear All,
I am calculating RESP charges using Antechamber of iron-sulfur cluster
complex. I used BS-DFT to optimize the geometry and UHF/6-31G* to
calculate ESP with the same wave function. But when I used antechamber
to get RESP charges using the following commands, it gave totally
different charges, for ex. for Phosphorus it changes from positive to
negative. I used g03 to generate ESP and Amber12. Can you help me to
figure out this error. Why when I used Mol2 and PDB output file
format the results are different.
Case-1- antechamber -i isph_BS2_ESP.log -fi gout -o
isph_BS2_charges.mol2 -fo mol2 -c resp -nc -3 -m 1 -j 0
Case-2- antechamber -i isph_BS2_ESP.log -fi gout -o
isph_BS2_charges.pdb -fo pdb -c resp -nc -3 -m 1 -j 0
case-1 case-2
1 H1 -2.7348 5.7385 -0.8702 H1 1 MOL
0.033219 -0.022303
2 C1 -2.5036 4.6673 -1.0416 C1 1 MOL
-0.006299 0.223724
3 H2 -3.4415 4.1405 -1.2117 H2 1 MOL
0.033219 -0.022303
4 H3 -1.9101 4.5871 -1.9546 H3 1 MOL
0.033219 -0.022303
5 S1 -1.6066 3.8893 0.3720 S1 1 MOL
-0.707521 -0.800886
6 H4 -3.3050 -1.4034 5.5582 H4 1 MOL
0.033219 -0.022303
7 C2 -2.9799 -1.2191 4.5082 C2 1 MOL
-0.006299 0.223724
8 H5 -2.3867 -0.3060 4.4967 H5 1 MOL
0.033219 -0.022303
9 H6 -2.3121 -2.0323 4.2283 H6 1 MOL
0.033219 -0.022303
10 S2 -4.3120 -1.1069 3.2118 S2 1 MOL
-0.707521 -0.800886
11 H7 -5.1424 -2.6200 -4.3101 H7 1 MOL
0.033219 -0.022303
12 C3 -4.8240 -2.0589 -3.4127 C3 1 MOL
-0.006299 0.223724
13 H8 -5.6519 -1.4230 -3.0942 H8 1 MOL
0.033219 -0.022303
14 H9 -4.6241 -2.7705 -2.6120 H9 1 MOL
0.033219 -0.022303
15 S3 -3.3258 -1.0246 -3.7285 S3 1 MOL
-0.707521 -0.800886
16 C4 1.6353 -2.2124 1.1152 C4 1 MOL
0.347237 0.223724
17 O1 0.9116 -2.2227 -0.1518 O1 1 MOL
-0.700173 -0.302119
18 C5 2.2372 -0.7879 1.2410 C5 1 MOL
-0.071025 0.223724
19 C6 2.3257 0.0024 0.1730 C6 1 MOL
0.086187 0.223724
20 C7 2.8221 1.4245 0.2108 C7 1 MOL
0.060883 0.223724
21 O2 3.9728 1.6405 -0.5892 O2 1 MOL
-0.524297 -0.302119
22 P1 5.4882 1.4598 0.1036 P1 1 MOL
1.268858 -0.137089
23 O3 5.5282 -0.1673 0.3453 O3 1 MOL
-0.584555 -0.302119
24 P2 6.1049 -1.3333 -0.6581 P2 1 MOL
1.447997 -0.137089
25 O4 5.1335 -2.6035 -0.1127 O4 1 MOL
-0.810740 -0.302119
26 O5 7.5113 -1.6974 -0.2624 O5 1 MOL
-0.860675 -0.302119
27 O6 5.7280 -1.0215 -2.0787 O6 1 MOL
-0.860675 -0.302119
28 O7 5.4889 2.0252 1.5043 O7 1 MOL
-0.816971 -0.302119
29 O8 6.4606 1.8761 -0.9688 O8 1 MOL
-0.816971 -0.302119
30 C8 2.7089 -0.2368 2.5772 C8 1 MOL
-0.328186 0.223724
31 H10 2.4023 -2.9928 1.1206 H10 1 MOL
0.033638 -0.022303
32 H11 0.9627 -2.4548 1.9504 H11 1 MOL
0.033638 -0.022303
33 H12 0.2705 -2.8033 0.4650 H12 1 MOL
0.244208 -0.022303
34 H13 2.0713 -0.3784 -0.8125 H13 1 MOL
0.095202 -0.022303
35 H14 2.0295 2.0676 -0.1968 H14 1 MOL
0.115549 -0.022303
36 H15 2.9883 1.7554 1.2434 H15 1 MOL
0.115549 -0.022303
37 H16 3.4730 0.5221 2.4322 H16 1 MOL
0.096618 -0.022303
38 H17 1.8969 0.2258 3.1623 H17 1 MOL
0.096618 -0.022303
39 H18 3.1366 -1.0374 3.1853 H18 1 MOL
0.096618 -0.022303
40 H19 4.2060 -2.3440 -0.2118 H19 1 MOL
0.377654 -0.022303
41 Fe1 -1.8353 1.6678 -0.0293 Fe1 1 MOL
1.044820 0.982822
42 Fe2 -0.5794 -0.8762 0.0259 Fe2 1 MOL
1.044820 0.982822
43 Fe3 -2.7635 -0.4471 -1.5904 Fe3 1 MOL
1.044820 0.982822
44 Fe4 -3.1684 -0.5310 1.2806 Fe4 1 MOL
1.044820 0.982822
45 S4 -0.7199 0.6552 -1.8014 S4 1 MOL
-0.869744 -0.800886
46 S5 -2.5692 -2.2740 -0.1602 S5 1 MOL
-0.869744 -0.800886
47 S6 -1.0930 0.4782 1.8149 S6 1 MOL
-0.869744 -0.800886
48 S7 -4.0748 1.0308 -0.3227 S7 1 MOL
-0.869744 -0.800886
The spin densities in case of DFT-B3lyp
41 Fe -4.814404
42 Fe -4.555871
43 Fe 4.669129
44 Fe 4.644358
The spin densities in case of UHF
41 Fe -4.664168
42 Fe -4.008851
43 Fe 4.026178
44 Fe 4.694864
Best regards,
Safwat
--
-----------------------------------------------------------
Safwat Abdel-Azeim, PhD
Computational Chemistry (Modeling of Biomolecules)
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Received on Mon Mar 11 2013 - 03:00:02 PDT
