********> bugfix.12
Author: Dave Case
Date: 08/21/2009

Programs: LEaP, force fields

Description: update the ff99SB and ff99bsc0 leaprc files to handle PDB
             format 3 atom and residue names

Usage: Use this patch to update amber10/dat/leap/cmd/leaprc.ff99{SB,bsc0}:

------------------------------------------------------------------------------
--- leaprc.ff99SB	15 Apr 2008 23:02:36 -0000	10.0
+++ leaprc.ff99SB	17 Jun 2009 11:55:47 -0000	10.2
@@ -1,6 +1,7 @@
 logFile leap.log
 #
 # ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field
+# -----  this file is updated for PDB format 3
 #
 #	load atom type hybridizations
 #
@@ -38,7 +39,6 @@
 	{ "CD"  "C" "sp2" }
 	{ "CE"  "C" "sp2" }
 	{ "CF"  "C" "sp2" }
-	{ "CG"  "C" "sp2" }
 	{ "CP"  "C" "sp2" }
 	{ "CI"  "C" "sp2" }
 	{ "CJ"  "C" "sp2" }
@@ -131,18 +131,14 @@
   { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
   { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
   { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
-  { 0 "G" "DG5"  } { 1 "G" "DG3"  } { "G" "DG" } { "GN" "DGN" }
-  { 0 "A" "DA5"  } { 1 "A" "DA3"  } { "A" "DA" } { "AN" "DAN" }
-  { 0 "C" "DC5"  } { 1 "C" "DC3"  } { "C" "DC" } { "CN" "DCN" }
-  { 0 "T" "DT5"  } { 1 "T" "DT3"  } { "T" "DT" } { "TN" "DTN" }
-  { 0 "C5" "DC5" }
-  { 0 "G5" "DG5" }
-  { 0 "A5" "DA5" }
-  { 0 "T5" "DT5" }
-  { 1 "C3" "DC3" }
-  { 1 "G3" "DG3" }
-  { 1 "A3" "DA3" }
-  { 1 "T3" "DT3" }
+  { 0 "G" "RG5"  } { 1 "G" "RG3"  } { "G" "RG" } { "GN" "RGN" }
+  { 0 "A" "RA5"  } { 1 "A" "RA3"  } { "A" "RA" } { "AN" "RAN" }
+  { 0 "C" "RC5"  } { 1 "C" "RC3"  } { "C" "RC" } { "CN" "RCN" }
+  { 0 "U" "RU5"  } { 1 "U" "RU3"  } { "U" "RU" } { "UN" "RUN" }
+  { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }  
+  { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }  
+  { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }  
+  { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }
 
 }
 
@@ -156,17 +152,26 @@
   { "C2*" "C2'" }
   { "C1*" "C1'" }
   { "C5M" "C7"  }
+  { "O2*" "O2'" }
   { "H1*" "H1'" }
   { "H2*1" "H2'1" }
   { "H2*2" "H2'2" }
+  { "H2'"  "H2'1" }
+  { "H2''" "H2'2" }
   { "H3*" "H3'" }
   { "H4*" "H4'" }
   { "H5*1" "H5'1" }
   { "H5*2" "H5'2" }
-# old ff atom names -> new
+  { "H5'"  "H5'1" }
+  { "H5''" "H5'2" }
+  { "HO2'" "HO'2" }
+  { "HO5'" "H5T" }
+  { "HO3'" "H3T" }
   { "O1'" "O4'" }
   { "OA"  "O1P" }
   { "OB"  "O2P" }
+  { "OP1" "O1P" }
+  { "OP2" "O2P" }
 }
 

--- leaprc.ff99bsc0	30 May 2008 16:10:02 -0000	10.1
+++ leaprc.ff99bsc0	17 Jun 2009 11:55:47 -0000	10.3
@@ -1,7 +1,8 @@
 logFile leap.log
 #
 # ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field
-#       using parmbsc0 for nucleic acids (assumed to be DNA)
+#       using parmbsc0 for nucleic acid.
+# ----- NOTE: this is designed for PDB format 3!
 #
 #	load atom type hybridizations
 #
@@ -39,7 +40,6 @@
 	{ "CD"  "C" "sp2" }
 	{ "CE"  "C" "sp2" }
 	{ "CF"  "C" "sp2" }
-	{ "CG"  "C" "sp2" }
 	{ "CP"  "C" "sp2" }
 	{ "CI"  "C" "sp2" }
 	{ "CJ"  "C" "sp2" }
@@ -134,18 +134,14 @@
   { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
   { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
   { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
-  { 0 "G" "DG5"  } { 1 "G" "DG3"  } { "G" "DG" } { "GN" "DGN" }
-  { 0 "A" "DA5"  } { 1 "A" "DA3"  } { "A" "DA" } { "AN" "DAN" }
-  { 0 "C" "DC5"  } { 1 "C" "DC3"  } { "C" "DC" } { "CN" "DCN" }
-  { 0 "T" "DT5"  } { 1 "T" "DT3"  } { "T" "DT" } { "TN" "DTN" }
-  { 0 "DC" "DC5" }
-  { 0 "DG" "DG5" }
-  { 0 "DA" "DA5" }
-  { 0 "DT" "DT5" }
-  { 1 "DC" "DC3" }
-  { 1 "DG" "DG3" }
-  { 1 "DA" "DA3" }
-  { 1 "DT" "DT3" }
+  { 0 "G" "RG5"  } { 1 "G" "RG3"  } { "G" "RG" } { "GN" "RGN" }
+  { 0 "A" "RA5"  } { 1 "A" "RA3"  } { "A" "RA" } { "AN" "RAN" }
+  { 0 "C" "RC5"  } { 1 "C" "RC3"  } { "C" "RC" } { "CN" "RCN" }
+  { 0 "U" "RU5"  } { 1 "U" "RU3"  } { "U" "RU" } { "UN" "RUN" }
+  { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }  
+  { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }  
+  { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }  
+  { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }  
 
 }
 
@@ -157,23 +153,29 @@
   { "C3*" "C3'" }
   { "O3*" "O3'" }
   { "C2*" "C2'" }
+  { "O2*" "O2'" }
   { "C1*" "C1'" }
   { "C5M" "C7"  }
   { "H1*" "H1'" }
   { "H2*1" "H2'1" }
   { "H2*2" "H2'2" }
-  { "H2'" "H2'1" }
+  { "H2'"  "H2'1" }
   { "H2''" "H2'2" }
   { "H3*" "H3'" }
   { "H4*" "H4'" }
   { "H5*1" "H5'1" }
   { "H5*2" "H5'2" }
-  { "H5'" "H5'1" }
+  { "H5'"  "H5'1" }
   { "H5''" "H5'2" }
-  { "OP1"  "O1P" }
-  { "OP2"  "O2P" }
+  { "HO2'" "HO'2" }
   { "HO5'" "H5T" }
   { "HO3'" "H3T" }
+# old ff atom names -> new
+  { "O1'" "O4'" }
+  { "OA"  "O1P" }
+  { "OB"  "O2P" }
+  { "OP1" "O1P" }
+  { "OP2" "O2P" }
 }
 
 
 
------------------------------------------------------------------------------
Workarounds: none