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 issue of Patching 2 sugar molecules
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Joined: Nov 2019
Posts: 46
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OP
Forum Member
Joined: Nov 2019
Posts: 46 |
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.
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 Re: issue of Patching 2 sugar molecules
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Joined: Sep 2003
Posts: 8,527 Likes: 2
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Joined: Sep 2003
Posts: 8,527 Likes: 2 |
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
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 Re: issue of Patching 2 sugar molecules
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Joined: Nov 2019
Posts: 46
Forum Member
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OP
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Joined: Nov 2019
Posts: 46 |
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.
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 Re: issue of Patching 2 sugar molecules
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Joined: Sep 2003
Posts: 8,527 Likes: 2
Forum Member
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Joined: Sep 2003
Posts: 8,527 Likes: 2 |
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 C3Each of the 3 atoms specified must be bonded to at least one of the other two.
Rick Venable computational chemist
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 Re: issue of Patching 2 sugar molecules
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Joined: Nov 2019
Posts: 46
Forum Member
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OP
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Joined: Nov 2019
Posts: 46 |
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.
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