Mercurial > repos > marpiech > norwich_tools
diff tools/rdock/data/sf/RbtInterIdxSF.prm @ 0:bc03dbb6eb37 draft
planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
| author | marpiech |
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| date | Mon, 29 Aug 2016 03:38:13 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/rdock/data/sf/RbtInterIdxSF.prm Mon Aug 29 03:38:13 2016 -0400 @@ -0,0 +1,126 @@ +RBT_PARAMETER_FILE_V1.00 +TITLE Intermolecular scoring function (without SOLVATION, indexed VDW) +VERSION $Id: //depot/dev/client3/rdock/2013.1/data/sf/RbtInterIdxSF.prm#3 $ + +################################################################################ +# Constant scoring function +# Represents loss of translation, rotational entropy of ligand +# DM 14 June 2006 - also calculates solvent penalty for all enabled solvent +# SOLVENT_PENALTY is defined as a fraction of the ligand binding penalty +# i.e. ligand binding penalty = 1.0 * WEIGHT +# solvent binding penalty = N(enabled solvent) * SOLVENT_PENALTY * WEIGHT +# 0.37 * 5.4 = 2.0 kJ/mol, which corresponds to GOLD Chemscore penalty +# Verdonk et al, J. Med. Chem. 2005 (48) 6504-6515 +SECTION CONST + SCORING_FUNCTION RbtConstSF + SOLVENT_PENALTY 0.37 + WEIGHT +5.4 +END_SECTION + +################################################################################ +# Rotational scoring function +# Represents loss of torsional entropy of ligand +SECTION ROT + SCORING_FUNCTION RbtRotSF + WEIGHT +1.0 +END_SECTION + +################################################################################ +# Pseudo SFs for setting up atomic attributes for polar and lipo atoms +SECTION SETUP_POLAR + SCORING_FUNCTION RbtSetupPolarSF + RADIUS 5.0 + NORM 25 + POWER 0.5 + CHGFACTOR 0.5 + GUANFACTOR 0.5 +END_SECTION + +################################################################################ +# Hydrogen-bond scoring function (also Metal-acceptor, C.cat - acceptor) +SECTION POLAR + SCORING_FUNCTION RbtPolarIdxSF + WEIGHT 3.4 + R12FACTOR 1.0 + R12INCR 0.05 + DR12MIN 0.25 + DR12MAX 0.6 + A1 180.0 + DA1MIN 30.0 + DA1MAX 80.0 + A2 180.0 + DA2MIN 60.0 + DA2MAX 100.0 + INCMETAL TRUE + INCHBD TRUE + INCHBA TRUE + INCGUAN TRUE + GUAN_PLANE TRUE + ABS_DR12 TRUE + GRIDSTEP 0.5 + RANGE 5.31 + INCR 3.36 + ATTR TRUE + LP_OSP2 TRUE + LP_PHI 45 + LP_DPHIMIN 15 + LP_DPHIMAX 30 + LP_DTHETAMIN 20 + LP_DTHETAMAX 60 +END_SECTION + +################################################################################ +# Repulsive polar scoring function (donor-donor, acceptor-acceptor, metal-donor, C.cat-donor etc) +SECTION REPUL + SCORING_FUNCTION RbtPolarIdxSF + WEIGHT 5.0 + R12FACTOR 1.0 + R12INCR 0.6 + DR12MIN 0.25 + DR12MAX 1.1 + A1 180.0 + DA1MIN 30.0 + DA1MAX 60.0 + A2 180.0 + DA2MIN 30.0 + DA2MAX 60.0 + INCMETAL TRUE + INCHBD TRUE + INCHBA TRUE + INCGUAN TRUE + GUAN_PLANE FALSE + ABS_DR12 FALSE + GRIDSTEP 0.5 + RANGE 5.32 + INCR 3.51 + ATTR FALSE + LP_OSP2 FALSE +END_SECTION + +################################################################################ +# Aromatic (pi-pi) scoring function, also used for cation-pi +#SECTION AROM +# SCORING_FUNCTION RbtAromIdxSF +# WEIGHT -1.8 +# R12 3.5 +# DR12MIN 0.25 +# DR12MAX 0.6 +# DAMIN 20.0 +# DAMAX 30.0 +# GRIDSTEP 0.5 +# RANGE 4.1 +# INCR 4.1 +#END_SECTION + +################################################################################ +# Van der Waals scoring function +SECTION VDW + SCORING_FUNCTION RbtVdwIdxSF + WEIGHT 1.0 + USE_4_8 FALSE + USE_TRIPOS FALSE + RMAX 1.5 + ECUT 120.0 + E0 1.5 + FAST_SOLVENT TRUE +END_SECTION