Merge branch 'main' into amjjbonvin-patch-1

.github/dependabot.yml

@@ -8,4 +8,4 @@ updates:
   - package-ecosystem: "pip" # See documentation for possible values
     directory: "/" # Location of package manifests
     schedule:
-      interval: "weekly"
+      interval: "monthly"

examples/thirdparty/openmm/openmm-implicit-solvent-test.cfg

@@ -29,8 +29,8 @@ implicit_solvent = true
 implicit_solvent_model = 'implicit/obc1.xml'
 timestep_ps = 0.002
 constraints = 'HBonds'
-equilibration_timesteps = 2000
-simulation_timesteps = 10000
+equilibration_timesteps = 100
+simulation_timesteps = 200
 
 # ====================================================================
 

examples/thirdparty/openmm/openmm-test.cfg

@@ -29,8 +29,8 @@ forcefield = 'amber14-all.xml'
 explicit_solvent_model = 'amber14/tip3p.xml'
 timestep_ps = 0.002
 constraints = 'HBonds'
-equilibration_timesteps = 2000
-simulation_timesteps = 10000
+equilibration_timesteps = 100
+simulation_timesteps = 200
 
 # ====================================================================
 

examples/thirdparty/openmm/openmm-topoaa-flexref-test.cfg

@@ -30,6 +30,9 @@ hise_1 = 113
 ambig_fname="data/ambig.tbl"
 sampling = 5
 
+[seletop]
+select = 1
+
 [caprieval]
 reference_fname = "data/1nx1_refe.pdb"
 
@@ -38,8 +41,8 @@ forcefield = 'amber14-all.xml'
 explicit_solvent_model = 'amber14/tip3p.xml'
 timestep_ps = 0.002
 constraints = 'HBonds'
-equilibration_timesteps = 200
-simulation_timesteps = 1000
+equilibration_timesteps = 100
+simulation_timesteps = 200
 
 [topoaa]
 
@@ -62,5 +65,6 @@ ssdihed = "alphabeta"
 
 [caprieval]
 reference_fname = "data/1nx1_refe.pdb"
+
 # ====================================================================
 

pyproject.toml

@@ -48,12 +48,12 @@ dependencies = [
 
 [project.optional-dependencies]
 dev = [
-  "coverage==7.6.4",
+  "coverage==7.6.7",
   "pytest==8.3.3",
   "pytest-cov==6.0.0",
-  "hypothesis==6.118.7",
+  "hypothesis==6.119.3",
   "pytest-mock==3.14.0",
-  "fastapi==0.115.4",
+  "fastapi==0.115.5",
   "httpx==0.27.2",
   "mpi4py==4.0.1",
   "kaleido==0.2.1",

src/haddock/cns/toppar/carbohydrate.param

@@ -57,6 +57,7 @@ BOND CCA  NH1    1000.0    1.45   !as extended atom carbon-N
 BOND CCS  C      1000.0    1.52   !"    "       "     "   -C
 BOND CCE  C      1000.0    1.52
 BOND CCA  C      1000.0    1.52
+BOND CC6  OC     1000.0    1.25   ! standard CO bond (parm10)
 
 
 ANGLe H    OH1  CCS   500.0   109.35
@@ -148,6 +149,10 @@ ANGLe C    CCE  OES   500.0   107.24
 ANGLe C    CCA  OES   500.0   107.24
 ANGLe C    CCE  CCS   500.0   108.72
 ANGLe C    CCA  CCS   500.0   108.72
+! other angles
+ANGLe OC   CC6  OC    500.00  123.3548
+ANGLe CCS  CC6  OC    500.0   109.70 ! guess from CCS-CC6-OAS (to check: experimental structures have 112-113)
+
 
 
 DIHEdral  X    CCS   CCS   X      2.0  3   0.0
@@ -174,6 +179,7 @@ DIHEdral  X    C     CCA   X      2.0  3   0.0
 DIHEdral  X    C     CCS   X      2.0  3   0.0 ! N-acetyl in NAG, 8/30/93
 DIHEdral  CCS  NH1   C     CCS    2.0  2   0.0 ! peptide plane in NAG
                                                !   guess - PDA 8/99
+DIHEdral  CCS  OES   CCE   CCS    2.0  2   0.0 ! guessing for BDP
 
 IMPRoper  CCS X    X    CCS    500.0     0  35.26439 
 IMPRoper  CCE X    X    CCS    500.0     0  35.26439 
@@ -205,6 +211,7 @@ IMPRoper  HAS CCE  OAS  CCS    500.00    0  66.8
 IMPRoper  HAS HAS  CCE  CCS    500.00    0  70.3 !SIA C3
 IMPRoper  HAS HAS  CCS  CCE    500.00    0  70.3 !SIA C3
 IMPRoper  HAS HAS  CCA  CCS    500.00    0  70.3
+IMPRoper  HAS HAS  CCS  CCS    500.00    0  70.3 !ABE C3
 IMPRoper  HAS OH1  CCS  CCS    500.00    0  66.9 !MAN,GLC,GLA,NAG,FCA,XYP C3 - A2G,FCA,SIA C4 - SIA C7,C8
 IMPRoper  HAS OAS  CCS  CCS    500.00    0  66.9
 IMPRoper  HAS CCS  OH1  CCS    500.00    0  66.8 !FUC C3 MAN,GLC,GLA,NAG,FUC,XYP C4
@@ -231,6 +238,8 @@ IMPRoper  HAS OES  OAS  CCS    500.00    0  67.6 !A12,A13,A14,A16,B12L,B14L alph
 IMPRoper  C   CCS  NH1  O      500.00    0   0.0 !NAG,SIA planar
 IMPRoper  NH1 C    CCS  H      500.00    0   0.0 !NAG,SIA planar
 IMPRoper  CCS NH1  C    CCS    500.00    0 180.0 !NAG,SIA trans peptide
+! new impropers
+IMPRoper  CC6 CCS  OC   OC     500.00    0   0.0 !BDP, angle taken from charmm
 
 
 {Asn-NAG}