Mercurial > repos > marpiech > norwich_tools_docking
diff tools/rdock/data/sf/RbtIonicAtoms.prm @ 3:b02d74d22d05 draft default tip
planemo upload
| author | marpiech |
|---|---|
| date | Mon, 29 Aug 2016 08:23:52 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/rdock/data/sf/RbtIonicAtoms.prm Mon Aug 29 08:23:52 2016 -0400 @@ -0,0 +1,197 @@ +RBT_PARAMETER_FILE_V1.00 +TITLE Receptor ionic atom definitions +VERSION $Id: //depot/dev/client3/rdock/2013.1/data/sf/RbtIonicAtoms.prm#2 $ +################################################################################ +# +# Revision history: +# +# 21 Nov 2001 (DM) Added Heme Fe entries +# 19 Oct 2001 (DM) Extended list of metal ions +# 13 Jun 2000 (DM) Branched from RbtRNAScoringFunction.prm +# New format for ionic atoms (separate section for each residue) +# +################################################################################ +# Formal charges for RNA atoms +# +# A/ADE +# +SECTION A + O1P -0.5 + O2P -0.5 +END_SECTION + +SECTION ADE + O1P -0.5 + O2P -0.5 +END_SECTION +# +# C/CYT +# +SECTION C + O1P -0.5 + O2P -0.5 +END_SECTION + +SECTION CYT + O1P -0.5 + O2P -0.5 +END_SECTION +# +# G/GUA +# +SECTION G + O1P -0.5 + O2P -0.5 +END_SECTION + +SECTION GUA + O1P -0.5 + O2P -0.5 +END_SECTION +# +# U/URA +# +SECTION U + O1P -0.5 + O2P -0.5 +END_SECTION + +SECTION URA + O1P -0.5 + O2P -0.5 +END_SECTION + +################################################################################# +# Formal charges for amino acids +# +# LYS+ +# +SECTION LYS + HZ1 +0.333 + HZ2 +0.333 + HZ3 +0.333 +END_SECTION +# +# ARG+ +# +SECTION ARG + HE +0.167 + HH11 +0.167 + HH12 +0.167 + HH21 +0.167 + HH22 +0.167 + CZ +0.167 +END_SECTION +# +# HSP+ +# +SECTION HSP + HD1 +0.333 + HE2 +0.333 + CE1 +0.333 +END_SECTION + +SECTION HIS + MANDATORY HD1,HE2 + HD1 +0.333 + HE2 +0.333 + CE1 +0.333 +END_SECTION +# +# ASP- +# +SECTION ASP + FORBIDDEN HD1,HD2 + OD1 -0.5 + OD2 -0.5 +END_SECTION +# +# GLU- +# +SECTION GLU + FORBIDDEN HE1,HE2 + OE1 -0.5 + OE2 -0.5 +END_SECTION + +################################################################################# +# Formal charges for metal cations +# +SECTION NA + NA +1.0 +END_SECTION + +SECTION MG + MG +1.0 +END_SECTION + +SECTION K + K +1.0 +END_SECTION + +SECTION CA + CA +1.0 +END_SECTION + +SECTION V + V +1.0 +END_SECTION + +SECTION MN + MN +1.0 +END_SECTION + +SECTION FE + FE +1.0 +END_SECTION + +# Specific entries for GOLD PDB test set +SECTION FS4 + FE1 +1.0 + FE2 +1.0 + FE3 +1.0 + FE4 +1.0 +END_SECTION + +SECTION HEM + FE +1.0 +END_SECTION + +SECTION NI + NI +1.0 +END_SECTION + +SECTION ZN + ZN +1.0 +END_SECTION + +# Specific entries for ASTEX MOL2 test set +SECTION HG + HG +1.0 +END_SECTION + +SECTION CD + CD +1.0 +END_SECTION + +SECTION FS + FE1 +1.0 + FE2 +1.0 + FE3 +1.0 + FE4 +1.0 +END_SECTION + +SECTION CO + CO +1.0 +END_SECTION + +#These metals occur in undefined residues +SECTION UNK + MG +1.0 + MN +1.0 + ZN +1.0 + FE1 +1.0 + FE2 +1.0 + FE3 +1.0 + FE4 +1.0 +END_SECTION