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issue of Patching 2 sugar molecules
#37716 11/21/19 08:57 AM
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Allen_123 Offline OP
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Allen_123
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Hello Charmm users,

I'm trying to model a lactose molecule using drude force field. I found that I need to use PATCH command to add a new bond between galactose and glucose. The command I used are follows

stream toppar_drude_master_protein_2013e.str
stream toppar_drude_carbohydrate_2013e.str
stream toppar_drude_model_2013e.str
open read card name "lactose.pdb" unit 21
read sequence pdb unit 21
generate CARB first none last none setup warn drude dmass 0.4
patch 14BA CARB 2 CARB 1 setup warn

The error message shows ' ERROR in PATIC: Residue 14BA was not found.' It is confusing since 14BA is just patch name not residue ID. The exact PATCH command worked when using regular charmm36 forcefield such as following:

open read card name "top_all36_carb.rtf" unit 25
read rtf card unit 25
close unit 25
open read card name "par_all36_carb.prm" unit 25
read parameter card unit 25 flex
close unit 25

open read card name "lactose.pdb" unit 21
read sequence pdb unit 21
generate CARB first none last none setup warn
!! 1beta galactose link 4alpha glucose
patch 14BA CARB 2 CARB 1 setup warn

I suspect it relates with DRUDE topology
I appreciate any help.
Thank you

Last edited by Allen_123; 11/21/19 09:15 AM.
Re: issue of Patching 2 sugar molecules
Allen_123 #37718 11/21/19 04:38 PM
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rmv Offline
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This post was moved; it was not in the appropriate forum for this topic.

None of the PRES definitions needed to create oligosaccharides are provided in toppar_drude_carbohydrate_2013e.str; the 00readme_drude.txt file suggests they'd be available in the fall of 2017, so they are overdue.

Rick Venable
computational chemist
Re: issue of Patching 2 sugar molecules
rmv #37719 11/22/19 02:22 AM
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Allen_123 Offline OP
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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.
Re: issue of Patching 2 sugar molecules
Allen_123 #37720 11/22/19 03:57 AM
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rmv Offline
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rmv
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The IC SEED command (intcor doc file) is needed before IC BUILD when the molecule has no defined coordinates yet. This might work:

ic seed CARB 1 C1 CARB 1 C2 CARB 1 C3

Each of the 3 atoms specified must be bonded to at least one of the other two.

Rick Venable
computational chemist
Re: issue of Patching 2 sugar molecules
Allen_123 #37721 11/22/19 07:05 AM
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Allen_123 Offline OP
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Thanks Rick!
It worked by using your command as well as moving 'coor sdrude and coor shake' after ic build.

Last edited by Allen_123; 11/22/19 08:05 AM.

Moderated by  alex, lennart, rmv 

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