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Merge pull request #714 from haddocking/glycan-1-6
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Glycan 1 6
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@amjjbonvin
amjjbonvin committed Oct 13, 2023
2 parents 51f6d42 + 49eed1e commit 4b38f64
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10 changes: 1 addition & 9 deletions CHANGELOG.md
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@@ -1,11 +1,3 @@
# Changelog

## new_version

* Updated the rigidbody sampling module by cleaning the CNS scripts and making them uptodate with the 2.4/2.5 version
* Created a new rigid-body example to test the updated implementation
* Added the model number to the generated CNS input scripts (used to define the random seed)
* Further cleaning of the modules, removed uncessary stuff
* Removed the iteration variable - not needed since each module has its own variables/default
* rigidbody now fully working without any errors at the CNS level

Will be edited as of the first main release
2 changes: 1 addition & 1 deletion examples/docking-antibody-antigen/docking-antibody-antigen-CDR-NMR-CSP-full.cfg
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Expand Up @@ -2,7 +2,7 @@
# Protein-protein docking example with NMR-derived ambiguous interaction restraints

# directory in which the scoring will be done
run_dir = "run1-CDR-NMR-CSP"
run_dir = "run1-CDR-NMR-CSP-full"

# compute mode
mode = "hpc"
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15 changes: 5 additions & 10 deletions examples/docking-protein-protein/docking-protein-protein-hpc-test.cfg
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Expand Up @@ -26,7 +26,6 @@ molecules = [
# Parameters for each stage are defined below, prefer full paths
# ====================================================================
[topoaa]
#tolerance = 20
autohis = false
[topoaa.mol1]
nhisd = 0
Expand All @@ -39,32 +38,28 @@ nhise = 1
hise_1 = 15

[rigidbody]
tolerance = 20
tolerance = 5
ambig_fname = "data/e2a-hpr_air.tbl"
sampling = 1000
sampling = 100

[caprieval]
#tolerance = 20
reference_fname = "data/e2a-hpr_1GGR.pdb"

[seletop]
#tolerance = 20
select = 200
select = 10

[flexref]
tolerance = 20
tolerance = 2
ambig_fname = "data/e2a-hpr_air.tbl"

[caprieval]
#tolerance = 20
reference_fname = "data/e2a-hpr_1GGR.pdb"

[emref]
tolerance = 20
tolerance = 2
ambig_fname = "data/e2a-hpr_air.tbl"

[caprieval]
#tolerance = 20
reference_fname = "data/e2a-hpr_1GGR.pdb"

# ====================================================================
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3 changes: 2 additions & 1 deletion examples/run_examples-full.py
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Expand Up @@ -58,7 +58,8 @@
("docking-protein-protein" , "docking-protein-protein-cltsel-full.cfg"), # noqa: E203, E501
("docking-protein-protein" , "docking-protein-protein-mdref-full.cfg"), # noqa: E203, E501
("docking-multiple-ambig" , "docking-multiple-tbls-clt-full.cfg"), # noqa: E203, E501
("docking-antibody-antigen" , "docking-antibody-antigen-CDR-accessible-full"), # noqa: E203, E501
("docking-antibody-antigen" , "docking-antibody-antigen-CDR-NMR-CSP-full.cfg"), # noqa: E203, E501
("docking-antibody-antigen" , "docking-antibody-antigen-CDR-accessible-full.cfg"), # noqa: E203, E501
("docking-antibody-antigen" , "docking-antibody-antigen-CDR-accessible-clt-full.cfg"), # noqa: E203, E501
("docking-antibody-antigen" , "docking-antibody-antigen-ranairCDR-full.cfg"), # noqa: E203, E501
("docking-antibody-antigen" , "docking-antibody-antigen-ranairCDR-clt-full.cfg"), # noqa: E203, E501
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2 changes: 2 additions & 0 deletions src/haddock/cns/toppar/par_axis.pro
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Expand Up @@ -14,4 +14,6 @@ NONBonded YY 0.01 0.01 0.01 0.01
NONBonded ZZ 0.01 0.01 0.01 0.01
NONBonded OO 0.01 0.01 0.01 0.01

IMPROPER XX YY OO ZZ 500.0 0 90.0

set message on echo on end
4 changes: 0 additions & 4 deletions src/haddock/cns/toppar/protein-allhdg5-4-noNter.link
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Expand Up @@ -2405,10 +2405,6 @@ link pept head - QSR tail + QSR end
link pctn head - QSR tail + CTN end
link pept head - QSR tail + NME end

first PROP tail + PRO end
first PROP tail + HYP end
first PROP tail + HY3 end

first ACET tail + ACE end

last CTER head - ALA end
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4 changes: 0 additions & 4 deletions src/haddock/cns/toppar/protein-allhdg5-4-noter.link
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Expand Up @@ -2405,10 +2405,6 @@ link pept head - QSR tail + QSR end
link pctn head - QSR tail + CTN end
link pept head - QSR tail + NME end

first PROP tail + PRO end
first PROP tail + HYP end
first PROP tail + HY3 end

first ACET tail + ACE end

set message=$old_message echo=$old_echo end
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3 changes: 3 additions & 0 deletions src/haddock/cns/toppar/protein-allhdg5-4.param
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Expand Up @@ -845,6 +845,7 @@ eval ($pd_v=$pd_x* 640.0) ANGLE HHAD NH_Y HHAB $pd_v 109.500
IMPRoper CH1E CH1E HA HA 500.00 {sd= 0.031} 0 -69.6639
IMPRoper CH1P CH1E HA HA 500.00 {sd= 0.031} 0 -69.6639
IMPRoper CH2E C N HA 500.00 {sd= 0.031} 0 67.7957
IMPRoper HA C N CH2E 500.00 {sd= 0.031} 0 67.7957
IMPRoper CH2E C NH1 H 500.00 {sd= 0.031} 0 0.0000 !c
IMPRoper CH2E N C HA 500.00 {sd= 0.031} 0 67.7957 ! d-amino acid
IMPRoper CH2E CCIS N HA 500.00 {sd= 0.031} 0 67.7957 ! cis pept
Expand Down Expand Up @@ -967,8 +968,10 @@ eval ($pd_v=$pd_x* 640.0) ANGLE HHAD NH_Y HHAB $pd_v 109.500
IMPRoper H C5 CRHH NH1 500.00 {sd= 0.031} 0 0.0282
IMPRoper H H C NH1 500.00 {sd= 0.031} 0 0.0032
IMPRoper H H C NH2 500.00 {sd= 0.031} 0 0.0032
IMPRoper HA C NH1 CH1E 500.00 {sd= 0.031} 0 66.1640
IMPRoper HA C NH1 CH2E 500.00 {sd= 0.031} 0 66.1640
IMPRoper HA CH1E HA HA 500.00 {sd= 0.031} 0 -66.5692
IMPRoper HA NH1 HA HA 500.00 {sd= 0.031} 0 -66.5692 ! added for NME CA improper, 6/8/23 Alexandre Bonvin
IMPRoper HA CH2E HA HA 500.00 {sd= 0.031} 0 -66.5934
IMPRoper HA HA CH1E OH1 500.00 {sd= 0.031} 0 -69.8494
IMPRoper HA HA CH1P OH1 500.00 {sd= 0.031} 0 -69.8494
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66 changes: 43 additions & 23 deletions src/haddock/cns/toppar/tensor.pdb
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@@ -1,25 +1,45 @@
REMARK FILENAME="/Users/abonvin/haddock2.1/toppar/tensor.pdb"
REMARK FILENAME="tensor.pdb"
REMARK topology file for dipolar coupling calculations
REMARK DATE:19-Nov-2007 11:56:26 created by user: abonvin
REMARK VERSION:1.2
ATOM 1 X ANI 995 3.000 0.000 0.000 1.00 0.00 ANI
ATOM 2 Y ANI 995 0.000 3.000 0.000 1.00 0.00 ANI
ATOM 3 Z ANI 995 0.000 0.000 3.000 1.00 0.00 ANI
ATOM 4 OO ANI 995 0.000 0.000 0.000 1.00 0.00 ANI
ATOM 5 X ANI 996 3.000 0.000 0.000 1.00 0.00 ANI
ATOM 6 Y ANI 996 0.000 3.000 0.000 1.00 0.00 ANI
ATOM 7 Z ANI 996 0.000 0.000 3.000 1.00 0.00 ANI
ATOM 8 OO ANI 996 0.000 0.000 0.000 1.00 0.00 ANI
ATOM 9 X ANI 997 3.000 0.000 0.000 1.00 0.00 ANI
ATOM 10 Y ANI 997 0.000 3.000 0.000 1.00 0.00 ANI
ATOM 11 Z ANI 997 0.000 0.000 3.000 1.00 0.00 ANI
ATOM 12 OO ANI 997 0.000 0.000 0.000 1.00 0.00 ANI
ATOM 13 X ANI 998 3.000 0.000 0.000 1.00 0.00 ANI
ATOM 14 Y ANI 998 0.000 3.000 0.000 1.00 0.00 ANI
ATOM 15 Z ANI 998 0.000 0.000 3.000 1.00 0.00 ANI
ATOM 16 OO ANI 998 0.000 0.000 0.000 1.00 0.00 ANI
ATOM 17 X ANI 999 3.000 0.000 0.000 1.00 0.00 ANI
ATOM 18 Y ANI 999 0.000 3.000 0.000 1.00 0.00 ANI
ATOM 19 Z ANI 999 0.000 0.000 3.000 1.00 0.00 ANI
ATOM 20 OO ANI 999 0.000 0.000 0.000 1.00 0.00 ANI
REMARK DATE:20-Jul-2022 20:50:45 created by user: abonvin
REMARK VERSION:1.3U
ATOM 1 X ANI 990 3.000 0.000 0.000 1.00 0.00 ANI
ATOM 2 Y ANI 990 0.000 3.000 0.000 1.00 0.00 ANI
ATOM 3 Z ANI 990 0.000 0.000 3.000 1.00 0.00 ANI
ATOM 4 OO ANI 990 0.000 0.000 0.000 1.00 0.00 ANI
ATOM 5 X ANI 991 3.000 0.000 0.000 1.00 0.00 ANI
ATOM 6 Y ANI 991 0.000 3.000 0.000 1.00 0.00 ANI
ATOM 7 Z ANI 991 0.000 0.000 3.000 1.00 0.00 ANI
ATOM 8 OO ANI 991 0.000 0.000 0.000 1.00 0.00 ANI
ATOM 9 X ANI 992 3.000 0.000 0.000 1.00 0.00 ANI
ATOM 10 Y ANI 992 0.000 3.000 0.000 1.00 0.00 ANI
ATOM 11 Z ANI 992 0.000 0.000 3.000 1.00 0.00 ANI
ATOM 12 OO ANI 992 0.000 0.000 0.000 1.00 0.00 ANI
ATOM 13 X ANI 993 3.000 0.000 0.000 1.00 0.00 ANI
ATOM 14 Y ANI 993 0.000 3.000 0.000 1.00 0.00 ANI
ATOM 15 Z ANI 993 0.000 0.000 3.000 1.00 0.00 ANI
ATOM 16 OO ANI 993 0.000 0.000 0.000 1.00 0.00 ANI
ATOM 17 X ANI 994 3.000 0.000 0.000 1.00 0.00 ANI
ATOM 18 Y ANI 994 0.000 3.000 0.000 1.00 0.00 ANI
ATOM 19 Z ANI 994 0.000 0.000 3.000 1.00 0.00 ANI
ATOM 20 OO ANI 994 0.000 0.000 0.000 1.00 0.00 ANI
ATOM 21 X ANI 995 3.000 0.000 0.000 1.00 0.00 ANI
ATOM 22 Y ANI 995 0.000 3.000 0.000 1.00 0.00 ANI
ATOM 23 Z ANI 995 0.000 0.000 3.000 1.00 0.00 ANI
ATOM 24 OO ANI 995 0.000 0.000 0.000 1.00 0.00 ANI
ATOM 25 X ANI 996 3.000 0.000 0.000 1.00 0.00 ANI
ATOM 26 Y ANI 996 0.000 3.000 0.000 1.00 0.00 ANI
ATOM 27 Z ANI 996 0.000 0.000 3.000 1.00 0.00 ANI
ATOM 28 OO ANI 996 0.000 0.000 0.000 1.00 0.00 ANI
ATOM 29 X ANI 997 3.000 0.000 0.000 1.00 0.00 ANI
ATOM 30 Y ANI 997 0.000 3.000 0.000 1.00 0.00 ANI
ATOM 31 Z ANI 997 0.000 0.000 3.000 1.00 0.00 ANI
ATOM 32 OO ANI 997 0.000 0.000 0.000 1.00 0.00 ANI
ATOM 33 X ANI 998 3.000 0.000 0.000 1.00 0.00 ANI
ATOM 34 Y ANI 998 0.000 3.000 0.000 1.00 0.00 ANI
ATOM 35 Z ANI 998 0.000 0.000 3.000 1.00 0.00 ANI
ATOM 36 OO ANI 998 0.000 0.000 0.000 1.00 0.00 ANI
ATOM 37 X ANI 999 3.000 0.000 0.000 1.00 0.00 ANI
ATOM 38 Y ANI 999 0.000 3.000 0.000 1.00 0.00 ANI
ATOM 39 Z ANI 999 0.000 0.000 3.000 1.00 0.00 ANI
ATOM 40 OO ANI 999 0.000 0.000 0.000 1.00 0.00 ANI
END
121 changes: 98 additions & 23 deletions src/haddock/cns/toppar/tensor.psf
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@@ -1,10 +1,10 @@
data_cns_mtf

_cns_mtf.title
; FILENAME="/Users/abonvin/haddock2.1/toppar/tensor.psf"
; FILENAME="tensor.psf"
topology file for dipolar coupling calculations
DATE:19-Nov-2007 11:56:26 created by user: abonvin
VERSION:1.2
DATE:20-Jul-2022 20:50:45 created by user: abonvin
VERSION:1.3U
;

loop_
Expand All @@ -16,26 +16,46 @@ _cns_mtf_atom.atom_name
_cns_mtf_atom.chemical_type
_cns_mtf_atom.charge
_cns_mtf_atom.atom_mass
1 'ANI' '995' 'ANI' 'X' 'XX' 0.00000 100.000
2 'ANI' '995' 'ANI' 'Y' 'YY' 0.00000 100.000
3 'ANI' '995' 'ANI' 'Z' 'ZZ' 0.00000 100.000
4 'ANI' '995' 'ANI' 'OO' 'OO' 0.00000 100.000
5 'ANI' '996' 'ANI' 'X' 'XX' 0.00000 100.000
6 'ANI' '996' 'ANI' 'Y' 'YY' 0.00000 100.000
7 'ANI' '996' 'ANI' 'Z' 'ZZ' 0.00000 100.000
8 'ANI' '996' 'ANI' 'OO' 'OO' 0.00000 100.000
9 'ANI' '997' 'ANI' 'X' 'XX' 0.00000 100.000
10 'ANI' '997' 'ANI' 'Y' 'YY' 0.00000 100.000
11 'ANI' '997' 'ANI' 'Z' 'ZZ' 0.00000 100.000
12 'ANI' '997' 'ANI' 'OO' 'OO' 0.00000 100.000
13 'ANI' '998' 'ANI' 'X' 'XX' 0.00000 100.000
14 'ANI' '998' 'ANI' 'Y' 'YY' 0.00000 100.000
15 'ANI' '998' 'ANI' 'Z' 'ZZ' 0.00000 100.000
16 'ANI' '998' 'ANI' 'OO' 'OO' 0.00000 100.000
17 'ANI' '999' 'ANI' 'X' 'XX' 0.00000 100.000
18 'ANI' '999' 'ANI' 'Y' 'YY' 0.00000 100.000
19 'ANI' '999' 'ANI' 'Z' 'ZZ' 0.00000 100.000
20 'ANI' '999' 'ANI' 'OO' 'OO' 0.00000 100.000
1 'ANI' '990' 'ANI' 'X' 'XX' 0.00000 100.000
2 'ANI' '990' 'ANI' 'Y' 'YY' 0.00000 100.000
3 'ANI' '990' 'ANI' 'Z' 'ZZ' 0.00000 100.000
4 'ANI' '990' 'ANI' 'OO' 'OO' 0.00000 100.000
5 'ANI' '991' 'ANI' 'X' 'XX' 0.00000 100.000
6 'ANI' '991' 'ANI' 'Y' 'YY' 0.00000 100.000
7 'ANI' '991' 'ANI' 'Z' 'ZZ' 0.00000 100.000
8 'ANI' '991' 'ANI' 'OO' 'OO' 0.00000 100.000
9 'ANI' '992' 'ANI' 'X' 'XX' 0.00000 100.000
10 'ANI' '992' 'ANI' 'Y' 'YY' 0.00000 100.000
11 'ANI' '992' 'ANI' 'Z' 'ZZ' 0.00000 100.000
12 'ANI' '992' 'ANI' 'OO' 'OO' 0.00000 100.000
13 'ANI' '993' 'ANI' 'X' 'XX' 0.00000 100.000
14 'ANI' '993' 'ANI' 'Y' 'YY' 0.00000 100.000
15 'ANI' '993' 'ANI' 'Z' 'ZZ' 0.00000 100.000
16 'ANI' '993' 'ANI' 'OO' 'OO' 0.00000 100.000
17 'ANI' '994' 'ANI' 'X' 'XX' 0.00000 100.000
18 'ANI' '994' 'ANI' 'Y' 'YY' 0.00000 100.000
19 'ANI' '994' 'ANI' 'Z' 'ZZ' 0.00000 100.000
20 'ANI' '994' 'ANI' 'OO' 'OO' 0.00000 100.000
21 'ANI' '995' 'ANI' 'X' 'XX' 0.00000 100.000
22 'ANI' '995' 'ANI' 'Y' 'YY' 0.00000 100.000
23 'ANI' '995' 'ANI' 'Z' 'ZZ' 0.00000 100.000
24 'ANI' '995' 'ANI' 'OO' 'OO' 0.00000 100.000
25 'ANI' '996' 'ANI' 'X' 'XX' 0.00000 100.000
26 'ANI' '996' 'ANI' 'Y' 'YY' 0.00000 100.000
27 'ANI' '996' 'ANI' 'Z' 'ZZ' 0.00000 100.000
28 'ANI' '996' 'ANI' 'OO' 'OO' 0.00000 100.000
29 'ANI' '997' 'ANI' 'X' 'XX' 0.00000 100.000
30 'ANI' '997' 'ANI' 'Y' 'YY' 0.00000 100.000
31 'ANI' '997' 'ANI' 'Z' 'ZZ' 0.00000 100.000
32 'ANI' '997' 'ANI' 'OO' 'OO' 0.00000 100.000
33 'ANI' '998' 'ANI' 'X' 'XX' 0.00000 100.000
34 'ANI' '998' 'ANI' 'Y' 'YY' 0.00000 100.000
35 'ANI' '998' 'ANI' 'Z' 'ZZ' 0.00000 100.000
36 'ANI' '998' 'ANI' 'OO' 'OO' 0.00000 100.000
37 'ANI' '999' 'ANI' 'X' 'XX' 0.00000 100.000
38 'ANI' '999' 'ANI' 'Y' 'YY' 0.00000 100.000
39 'ANI' '999' 'ANI' 'Z' 'ZZ' 0.00000 100.000
40 'ANI' '999' 'ANI' 'OO' 'OO' 0.00000 100.000
-1 ' ' ' ' ' ' ' ' ' ' -1.00000 -1.00000

loop_
Expand All @@ -56,6 +76,21 @@ _cns_mtf_bond.id[2]
17 20
18 20
19 20
21 24
22 24
23 24
25 28
26 28
27 28
29 32
30 32
31 32
33 36
34 36
35 36
37 40
38 40
39 40
-1 -1

loop_
Expand All @@ -77,6 +112,21 @@ _cns_mtf_angle.id[3]
17 20 18
17 20 19
18 20 19
21 24 22
21 24 23
22 24 23
25 28 26
25 28 27
26 28 27
29 32 30
29 32 31
30 32 31
33 36 34
33 36 35
34 36 35
37 40 38
37 40 39
38 40 39
-1 -1 -1

loop_
Expand Down Expand Up @@ -119,6 +169,26 @@ _cns_mtf_explicit_nonbonded_exclusion.iblo
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
-1

loop_
Expand All @@ -128,5 +198,10 @@ _cns_mtf_group_linked_list.first_atom_id
8
12
16
20
24
28
32
36
-1

10 changes: 10 additions & 0 deletions src/haddock/cns/toppar/tensor_para.psf
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Expand Up @@ -141,6 +141,16 @@ _cns_mtf_improper.id[1]
_cns_mtf_improper.id[2]
_cns_mtf_improper.id[3]
_cns_mtf_improper.id[4]
1 2 4 3
5 6 8 7
9 10 12 11
13 14 16 15
17 18 20 19
21 22 24 23
25 26 28 27
29 30 32 31
33 34 36 35
37 38 40 39
-1 -1 -1 -1

loop_
Expand Down
2 changes: 2 additions & 0 deletions src/haddock/cns/toppar/top_axis.pro
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Expand Up @@ -33,6 +33,8 @@ residue XAN
bond X OO
bond Y OO
bond Z OO

improper X Y OO Z
end

residue DAN
Expand Down
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