From ff3e9804befc5324fe7816fe46b0585487faee17 Mon Sep 17 00:00:00 2001 From: VGPReys Date: Fri, 20 Sep 2024 12:02:02 +0200 Subject: [PATCH] fix parameters in examples --- .../thirdparty/openmm/openmm-topoaa-flexref-test.cfg | 12 +++++++----- src/haddock/modules/refinement/openmm/defaults.yaml | 7 +++++-- 2 files changed, 12 insertions(+), 7 deletions(-) diff --git a/examples/thirdparty/openmm/openmm-topoaa-flexref-test.cfg b/examples/thirdparty/openmm/openmm-topoaa-flexref-test.cfg index ba5423609..92d509073 100644 --- a/examples/thirdparty/openmm/openmm-topoaa-flexref-test.cfg +++ b/examples/thirdparty/openmm/openmm-topoaa-flexref-test.cfg @@ -50,11 +50,13 @@ reference_fname = "data/1nx1_refe.pdb" tolerance = 20 ambig_fname = "data/ambig.tbl" # Define peptide as fully flexible -nfle2 = 2 -fle_sta_2_1 = 1 -fle_end_2_1 = 5 -fle_sta_2_2 = 6 -fle_end_2_2 = 11 +nfle = 2 +fle_sta_1 = 1 +fle_end_1 = 5 +fle_seg_1 = "B" +fle_sta_2 = 6 +fle_end_2 = 11 +fle_seg_2 = "B" # Define automatically dihedral restraints # for alpha and beta secondary structure elements ssdihed = "alphabeta" diff --git a/src/haddock/modules/refinement/openmm/defaults.yaml b/src/haddock/modules/refinement/openmm/defaults.yaml index 92456f732..004b97ed6 100644 --- a/src/haddock/modules/refinement/openmm/defaults.yaml +++ b/src/haddock/modules/refinement/openmm/defaults.yaml @@ -224,7 +224,9 @@ iniseed: max: 1000000 title: Simulation seed. short: Set a pseudo-random seed for the simulation. - long: Set a pseudo-random seed for the simulation. This defines how the initial velocities are created, but has no effect on the randomicity of the solvation box. + long: Set a pseudo-random seed for the simulation. This defines how the + initial velocities are created, but has no effect on the randomicity + of the solvation box. group: 'sampling' explevel: easy @@ -245,7 +247,8 @@ solv_equilibration: type: boolean title: Process the solvent equilibration phase. short: Process the solvent equilibration phase. - long: Process the solvent equilibration phase. If 'true', the solvent will be equilibrated while constraining proteins positions to intial ones. + long: Process the solvent equilibration phase. + If 'true', the solvent will be equilibrated while constraining proteins positions to intial ones. group: 'sampling' explevel: easy