Hello everyone,
is it ok to get dummy atoms in parametrzation using MCPB, I am getting errors while saving parameters while using this prep file and I am trying to understand what might be the problem.
There is some confusion that there are dummy atoms with DU type in prep file below.
Is that normal?
Best regards,
Andrew
1 1 2
Zn-CCCH fragment set created by MTK++/MCPB
CYSTEINE with negative charge
CY2 INT 1
CORR OMIT DU BEG
0.00000
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 N N M 3 2 1 1.335 116.600 180.000 -0.46300
5 HN H E 4 3 2 1.010 119.800 0.000 0.25200
6 CA CT M 4 3 2 1.449 121.900 180.000 0.03500
7 HA H1 E 6 4 3 1.090 109.500 300.000 0.04800
8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.32484
9 HB3 H1 E 8 6 4 1.090 109.500 60.000 0.17553
10 HB2 H1 E 8 6 4 1.090 109.500 300.000 0.17553
11 SG S2 E 8 6 4 1.810 116.000 180.000 -0.47287
12 C C M 6 4 3 1.522 111.100 180.000 0.61600
13 O O E 12 6 4 1.229 120.500 0.000 -0.50400
DONE
HISTIDINE EPSILONH
HE1 INT 1
CORR OMIT DU BEG
0.00000
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 N N M 3 2 1 1.335 116.600 180.000 -0.41570
5 H H E 4 3 2 1.010 119.800 0.000 0.27190
6 CA CT M 4 3 2 1.449 121.900 180.000 -0.05810
7 HA H1 E 6 4 3 1.090 109.500 300.000 0.13600
8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.39023
9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.17670
10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.17670
11 CG CC S 8 6 4 1.510 115.000 180.000 0.17220
12 ND1 N1 S 11 8 6 1.390 122.000 180.000 -0.21863
13 CE1 CR B 12 11 8 1.320 108.000 180.000 0.02565
14 HE1 H5 E 13 12 11 1.090 120.000 180.000 0.12545
15 NE2 NA B 13 12 11 1.310 109.000 0.000 -0.13860
16 HE2 H E 15 13 12 1.010 125.000 180.000 0.30074
17 CD2 CW S 15 13 12 1.360 110.000 0.000 -0.24025
18 HD2 H4 E 17 15 13 1.090 120.000 180.000 0.16438
19 C C M 6 4 3 1.522 111.100 180.000 0.59730
20 O O E 19 6 4 1.229 120.500 0.000 -0.56790
LOOP
CG CD2
IMPROPER
CA N H
CE1 CD2 NE2 HE2
CG NE2 CD2 HD2
ND1 NE2 CE1 HE1
DONE
Zinc(II) Ion
ZN2 INT 1
CORR OMIT DU BEG
0.00000
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 ZN ZN M 3 2 1 1.000 90.000 180.000 0.50194
DONE
STOP
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Received on Tue Nov 15 2011 - 02:00:03 PST
