Thank you for your response. The PATCH command worked by using toppar_drude_carbohydrate_2018a.str. But I am not able to build the cartesian coordinates of lactose using " i build" command although I have included all the necessary parameters.

open read card name "lactose.pdb" unit 21
read sequence pdb unit 21
stream toppar_drude_master_protein_2013e.str
stream toppar_drude_carbohydrate_2018a.str
stream toppar_drude_model_2013e.str
generate CARB first none last none setup warn drude dmass 0.4
patch 14BA CARB 2 CARB 1 setup warn
close unit 21
autogenerate angles dihedrals

ic para
ic build
coor sdrude
coor print

***** LEVEL 1 WARNING FROM *****
***** SOME COORDINATES NOT BUILT


1 1 BGAL C1 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
2 1 BGAL DC1 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
3 1 BGAL H1 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
4 1 BGAL C5 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
5 1 BGAL DC5 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
6 1 BGAL H5 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
7 1 BGAL O5 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
8 1 BGAL DO5 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
9 1 BGAL LP5A 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
10 1 BGAL LP5B 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
11 1 BGAL LPX5 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
12 1 BGAL C2 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
13 1 BGAL DC2 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
14 1 BGAL H2 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
15 1 BGAL O2 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
16 1 BGAL DO2 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
17 1 BGAL HO2 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
18 1 BGAL LP2A 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
19 1 BGAL LP2B 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
20 1 BGAL C3 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
21 1 BGAL DC3 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
22 1 BGAL H3 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
23 1 BGAL O3 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
24 1 BGAL DO3 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
25 1 BGAL HO3 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
26 1 BGAL LP3A 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
27 1 BGAL LP3B 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
28 1 BGAL C4 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
29 1 BGAL DC4 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
30 1 BGAL H4 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
31 1 BGAL O4 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
32 1 BGAL DO4 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
33 1 BGAL HO4 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
34 1 BGAL LP4A 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
35 1 BGAL LP4B 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
36 1 BGAL C6 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
37 1 BGAL DC6 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
38 1 BGAL H61 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
39 1 BGAL H62 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
40 1 BGAL O6 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
41 1 BGAL DO6 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
42 1 BGAL HO6 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
43 1 BGAL LP6A 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
44 1 BGAL LP6B 9999.0000000000 9999.0000000000 9999.0000000000 CARB 1 0.0000000000
45 2 AGLC C1 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
46 2 AGLC DC1 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
47 2 AGLC H1 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
48 2 AGLC O1 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
49 2 AGLC DO1 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
50 2 AGLC HO1 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
51 2 AGLC C5 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
52 2 AGLC DC5 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
53 2 AGLC H5 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
54 2 AGLC O5 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
55 2 AGLC DO5 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
56 2 AGLC LP1A 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
57 2 AGLC LP1B 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
58 2 AGLC LP5A 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
59 2 AGLC LP5B 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
60 2 AGLC LPX5 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
61 2 AGLC C2 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
62 2 AGLC DC2 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
63 2 AGLC H2 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
64 2 AGLC O2 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
65 2 AGLC DO2 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
66 2 AGLC HO2 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
67 2 AGLC LP2A 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
68 2 AGLC LP2B 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
69 2 AGLC C3 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
70 2 AGLC DC3 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
71 2 AGLC H3 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
72 2 AGLC O3 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
73 2 AGLC DO3 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
74 2 AGLC HO3 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
75 2 AGLC LP3A 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
76 2 AGLC LP3B 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
77 2 AGLC C4 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
78 2 AGLC DC4 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
79 2 AGLC H4 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
80 2 AGLC O4 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
81 2 AGLC DO4 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
82 2 AGLC C6 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
83 2 AGLC DC6 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
84 2 AGLC H61 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
85 2 AGLC H62 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
86 2 AGLC O6 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
87 2 AGLC DO6 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
88 2 AGLC HO6 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
89 2 AGLC LP6A 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
90 2 AGLC LP6B 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
91 2 AGLC LPDA4 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
92 2 AGLC LPDB4 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000
93 2 AGLC LPXD4 9999.0000000000 9999.0000000000 9999.0000000000 CARB 2 0.0000000000


Last edited by Allen_123; 11/22/19 03:50 AM.