Skip to content

remove duplicated parameter definitions in fragment_probes.param, protein-allhdg5-4.param and protein-CG-Martini-2-2.param #1590

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
amjjbonvin wants to merge 13 commits into
base: main
Choose a base branch
from
+1 −20,633
Open

remove duplicated parameter definitions in fragment_probes.param, protein-allhdg5-4.param and protein-CG-Martini-2-2.param #1590

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
13 commits
Select commit Hold shift + click to select a range
b5da6ee
Remove duplicate reverse-direction DIHEDRAL entries from Martini CG p…
amjjbonvin Jun 26, 2026
3c4d730
Remove duplicate BOND/ANGLE/DIHEDRAL entries from CG and all-atom par…
amjjbonvin Jun 26, 2026
adf0e31
Merge branch 'main' into martini-param-cleanup
amjjbonvin Jun 26, 2026
81180d5
Updated CHANGELOG
amjjbonvin Jun 26, 2026
78e9b28
Removed spurious lines (forgotten in previous edit)
amjjbonvin Jun 27, 2026
55cd95c
Merge branch 'main' into martini-param-cleanup
amjjbonvin Jun 27, 2026
b9b29cc
Corrected code for reading cg-to-as restraints - issue #1592
amjjbonvin Jun 27, 2026
c3d69cc
Merge branch 'martini-param-cleanup' of https://github.com/haddocking…
amjjbonvin Jun 27, 2026
e6a6b55
Update CHANGELOG with recent bug fixes and changes
amjjbonvin Jun 27, 2026
18593d2
Revert "Corrected code for reading cg-to-as restraints - issue #1592"
amjjbonvin Jun 29, 2026
9c08414
Reverted commit of the cgtoaa fix
amjjbonvin Jun 29, 2026
7fb8635
Merge branch 'main' into martini-param-cleanup
amjjbonvin Jun 29, 2026
0203485
Merge branch 'main' into martini-param-cleanup
amjjbonvin Jul 16, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
# Changelog

=======
- 2026-06-26: Removed duplicated definition in param files - Issue ##1589
- 2026-07-13: Added option to select models/clusters in reverse order - Issue #1620
- 2026-07-10: Corrected ranking in caprieval for reverse sorting - Issue #1621
- 2026-07-09: Added `deeprank` scoring module using deeprank-gnn-esm - Issue #569
Expand Down
49 changes: 0 additions & 49 deletions src/haddock/cns/toppar/fragment_probes.param
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -200,18 +200,12 @@ DIHEdral c3__ os__ c3__ h1__ 0.383 3 0.00
DIHEdral ca__ ca__ ca__ ca__ 3.625 2 180.00
DIHEdral ca__ ca__ ca__ ha__ 3.625 2 180.00
DIHEdral ca__ ca__ oh__ ho__ 0.900 2 180.00
DIHEdral h1__ c3__ n__ c__ 0.000 0 0.00
DIHEdral h1__ c3__ n__ c3__ 0.000 0 0.00
DIHEdral h1__ c3__ c3__ c3__ 0.156 3 0.00
DIHEdral h1__ c3__ c3__ hc__ 0.156 3 0.00
DIHEdral h1__ c3__ oh__ ho__ 0.167 3 0.00
DIHEdral h1__ c3__ os__ c3__ 0.383 3 0.00
DIHEdral h4__ c__ c3__ hc__ 0.000 2 180.00
DIHEdral h4__ c__ ca__ ca__ 1.000 2 180.00
DIHEdral ha__ ca__ ca__ ca__ 3.625 2 180.00
DIHEdral ha__ ca__ ca__ ha__ 3.625 2 180.00
DIHEdral hc__ c3__ c3__ c3__ 0.160 3 0.00
DIHEdral hc__ c3__ c3__ h1__ 0.156 3 0.00
DIHEdral hc__ c3__ c3__ hc__ 0.150 3 0.00
DIHEdral hn__ n3__ c3__ h1__ 0.300 3 0.00
DIHEdral n1__ c1__ c3__ hc__ 0.000 2 180.00
Expand All @@ -229,10 +223,6 @@ DIHEdral oh__ c3__ c3__ hc__ MULT 2 0.250 1 0.00
0.000 0 0.00
DIHEdral c3__ c3__ oh__ ho__ MULT 2 0.250 1 0.00
0.160 3 0.00
DIHEdral ho__ oh__ c3__ c3__ MULT 2 0.250 1 0.00
0.160 3 0.00
DIHEdral hc__ c3__ c3__ oh__ MULT 2 0.250 1 0.00
0.000 0 0.00

{ Proper Dihedrals: from Cagliari }
DIHEdral C_ CD_ N_ C_ 0.650 2 180.00
Expand Down Expand Up @@ -281,47 +271,30 @@ DIHEdral CT_ N_ C_ CT_ 2.500 2 180.00
DIHEdral CT_ N_ CT_ H1_ 0.000 0 0.00
DIHEdral CT_ S_ CM_ CT_ 1.100 2 180.00
DIHEdral CT_ CM_ CD_ N_ 6.650 2 180.00
DIHEdral CT_ CT_ C_ O_ 0.000 0 0.00
DIHEdral CT_ CT_ S_ CM_ 0.333 3 0.00
DIHEdral CT_ CT_ CT_ C_ 0.156 3 0.00
DIHEdral CT_ CT_ CT_ N_ 0.156 3 0.00
DIHEdral CT_ CT_ CT_ S_ 0.156 3 0.00
DIHEdral CT_ CT_ CT_ H1_ 0.156 3 0.00
DIHEdral CT_ CT_ CT_ HC_ 0.160 3 0.00
DIHEdral CT_ CT_ CT_ HP_ 0.156 3 0.00
DIHEdral CT_ CT_ CT_ N3_ 0.156 3 0.00
DIHEdral CT_ CT_ CT_ OH_ 0.156 3 0.00
DIHEdral CT_ CT_ N3_ H_ 0.156 3 0.00
DIHEdral CT_ CT_ N3_ CT_ 0.156 3 0.00
DIHEdral CT_ N3_ CT_ CT_ 0.156 3 0.00
DIHEdral CT_ N3_ CT_ HP_ 0.156 3 0.00
DIHEdral H1_ CT_ N_ C_ 0.000 0 0.00
DIHEdral H1_ CT_ N_ CT_ 0.000 0 0.00
DIHEdral H1_ CT_ S_ CM_ 0.333 3 0.00
DIHEdral H1_ CT_ CT_ C_ 0.156 3 0.00
DIHEdral H1_ CT_ CT_ S_ 0.156 3 0.00
DIHEdral H1_ CT_ CT_ CT_ 0.156 3 0.00
DIHEdral H1_ CT_ CT_ H1_ 0.156 3 0.00
DIHEdral H1_ CT_ CT_ HC_ 0.156 3 0.00
DIHEdral H1_ CT_ OH_ HO_ 0.167 3 0.00
DIHEdral HA_ CM_ NT_ H_ 0.300 2 180.00
DIHEdral HA_ CM_ NT_ CT_ 0.300 2 180.00
DIHEdral HC_ CT_ CT_ N_ 0.156 3 0.00
DIHEdral HC_ CT_ CT_ S_ 0.156 3 0.00
DIHEdral HC_ CT_ CT_ CT_ 0.160 3 0.00
DIHEdral HC_ CT_ CT_ H1_ 0.156 3 0.00
DIHEdral HC_ CT_ CT_ HC_ 0.150 3 0.00
DIHEdral HC_ CT_ CT_ HP_ 0.156 3 0.00
DIHEdral HC_ CT_ CT_ N3_ 0.156 3 0.00
DIHEdral HP_ CT_ CT_ S_ 0.156 3 0.00
DIHEdral HP_ CT_ CT_ CT_ 0.156 3 0.00
DIHEdral HP_ CT_ CT_ H1_ 0.156 3 0.00
DIHEdral HP_ CT_ N3_ H_ 0.156 3 0.00
DIHEdral HP_ CT_ N3_ CT_ 0.156 3 0.00
DIHEdral N3_ CT_ CT_ S_ 0.156 3 0.00
DIHEdral N3_ CT_ CT_ CT_ 0.156 3 0.00
DIHEdral N3_ CT_ CT_ H1_ 0.156 3 0.00
DIHEdral NT_ CM_ NT_ H_ 0.300 2 180.00
DIHEdral NT_ CM_ NT_ CT_ 0.300 2 180.00
DIHEdral NT_ CT_ CT_ S_ 0.156 3 0.00
DIHEdral NT_ CT_ CT_ H1_ 0.156 3 0.00
Expand All @@ -338,10 +311,6 @@ DIHEdral O_ C_ CT_ HC_ MULT 2 0.800 1 0.00
0.080 3 180.00
DIHEdral HC_ CT_ CT_ OH_ MULT 2 0.250 1 0.00
0.000 0 0.00
DIHEdral N_ C_ CT_ CT_ MULT 4 0.200 1 0.00
0.200 2 0.00
0.400 3 0.00
0.000 0 0.00
DIHEdral CM_ CD_ N_ C_ MULT 2 1.200 1 180.00
0.650 2 180.00
DIHEdral CM_ CD_ C_ O2_ MULT 2 2.175 2 180.00
Expand All @@ -350,10 +319,6 @@ DIHEdral CT_ CT_ OH_ HO_ MULT 2 0.250 1 0.00
0.160 3 0.00
DIHEdral CT_ S_ CM_ CD_ MULT 2 1.100 2 180.00
0.700 3 180.00
DIHEdral CT_ CT_ N_ C_ MULT 4 2.000 1 0.00
2.000 2 0.00
0.400 3 0.00
0.000 0 0.00
DIHEdral CT_ CT_ CT_ CT_ MULT 3 0.200 1 180.00
0.250 2 180.00
0.180 3 0.00
Expand All @@ -372,7 +337,6 @@ DIHEdral CT_ CD_ C_ CA_ 2.175 2 180.00
DIHEdral CD_ CT_ CT_ CA_ 0.156 3 0.00
DIHEdral CM_ CD_ C_ O_ MULT 2 2.175 2 180.00
0.300 3 0.00
DIHEdral HP_ CT_ CT_ HC_ 0.156 3 0.00
DIHEdral O_ C_ CD_ C_ 2.175 2 180.00
DIHEdral CA_ CA_ CA_ OH_ 3.625 2 180.00
DIHEdral C_ CA_ CA_ OH_ 3.625 2 180.00
Expand All @@ -389,18 +353,12 @@ DIHEdral CM_ CD_ CT_ HC_ 0.000 0 0.00
DIHEdral O_ C_ CT_ OH_ 0.000 0 0.00
DIHEdral CT_ N2_ CT_ H1_ 0.000 0 0.00
DIHEdral OH_ CM_ CD_ CT_ 6.650 2 180.00
DIHEdral CD_ CT_ CT_ HC_ 0.156 3 0.00
DIHEdral CT_ CT_ CT_ CM_ 0.156 3 0.00
DIHEdral CD_ C_ CT_ CT_ 0.000 0 0.00
DIHEdral CT_ CT_ CD_ C_ 0.000 0 0.00
DIHEdral C_ CT_ OH_ HO_ 0.167 3 0.00
DIHEdral CA_ CA_ N2_ CT_ 2.400 2 180.00
DIHEdral C_ CD_ C_ N_ 2.175 2 180.00
DIHEdral CA_ CA_ OH_ HO_ 0.900 2 180.00
DIHEdral CT_ CM_ CD_ C_ 6.650 2 180.00
DIHEdral C_ CD_ C_ O_ 2.175 2 180.00
DIHEdral CT_ CT_ CD_ CM_ 0.000 0 0.00
DIHEdral HO_ OH_ CA_ CA_ 0.900 2 180.00
DIHEdral C_ CA_ CA_ CT_ 3.625 2 180.00
DIHEdral HO_ OH_ CT_ CM_ 0.167 3 0.00
DIHEdral OH_ CA_ CA_ HA_ 3.625 2 180.00
Expand All @@ -410,26 +368,19 @@ DIHEdral CD_ C_ CT_ OH_ 0.000 0 0.00
DIHEdral OH_ CM_ CD_ C_ 6.650 2 180.00
DIHEdral CD_ C_ CT_ CM_ 0.000 0 0.00
DIHEdral CD_ C_ CT_ HP_ 0.000 0 0.00
DIHEdral N3_ CT_ CT_ HC_ 0.156 3 0.00
DIHEdral CT_ CT_ CT_ CA_ 0.156 3 0.00
DIHEdral OH_ CA_ CA_ CA_ 3.625 2 180.00
DIHEdral HO_ OH_ CM_ CD_ 1.050 2 180.00
DIHEdral CA_ CA_ CA_ HA_ 3.625 2 180.00
DIHEdral HA_ CA_ CA_ HA_ 3.625 2 180.00
DIHEdral CT_ CT_ CM_ CD_ 0.000 0 0.00
DIHEdral HC_ CT_ CT_ CM_ 0.156 3 0.00
DIHEdral CT_ CT_ CT_ CD_ 0.156 3 0.00
DIHEdral CA_ N2_ CT_ H1_ 0.000 0 0.00
DIHEdral O_ C_ CA_ CA_ 1.000 2 180.00
DIHEdral HA_ CA_ CA_ CA_ 3.625 2 180.00
DIHEdral CT_ CA_ CA_ N2_ 3.625 2 180.00
DIHEdral CT_ CT_ CA_ CA_ 0.000 0 0.00
DIHEdral CD_ C_ CT_ N3_ 0.000 0 0.00
DIHEdral CD_ C_ CA_ CA_ 3.625 2 180.00
DIHEdral OH_ CT_ CM_ OH_ 0.000 0 0.00
DIHEdral CD_ C_ N_ H_ 2.500 2 180.00
DIHEdral C_ CD_ CT_ CT_ 0.000 0 0.00
DIHEdral H1_ CT_ N2_ CT_ 0.000 0 0.00



Expand Down
Loading
Loading