Add leap dat files from AmberTools 15 release.

swails · Jun 24, 2015 · bd7f51a · bd7f51a
1 parent bc05c4f
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diff --git a/share/amber/dat/leap/cmd/leaprc.ff12SB b/share/amber/dat/leap/cmd/leaprc.ff12SB
@@ -164,7 +164,7 @@ addPdbResMap {
 # { 0 "GUA" "G5"  } { 1 "GUA" "G3"  } { "GUA" "G" }
 # { 0 "ADE" "A5"  } { 1 "ADE" "A3"  } { "ADE" "A" }
 # { 0 "CYT" "C5"  } { 1 "CYT" "C3"  } { "CYT" "C" }
-# { 0 "THY" "T5"  } { 1 "THY" "T3"  } { "THY" "T" }
+# { 0 "URA" "R5"  } { 1 "URA" "R3"  } { "URA" "R" }
 
 }
 

diff --git a/share/amber/dat/leap/cmd/leaprc.ff14SB b/share/amber/dat/leap/cmd/leaprc.ff14SB
@@ -163,7 +163,7 @@ addPdbResMap {
 # { 0 "GUA" "G5"  } { 1 "GUA" "G3"  } { "GUA" "G" }
 # { 0 "ADE" "A5"  } { 1 "ADE" "A3"  } { "ADE" "A" }
 # { 0 "CYT" "C5"  } { 1 "CYT" "C3"  } { "CYT" "C" }
-# { 0 "THY" "T5"  } { 1 "THY" "T3"  } { "THY" "T" }
+# { 0 "URA" "R5"  } { 1 "URA" "R3"  } { "URA" "R" }
 
 }
 

diff --git a/share/amber/dat/leap/cmd/leaprc.ff14SB.redq b/share/amber/dat/leap/cmd/leaprc.ff14SB.redq
@@ -0,0 +1,213 @@
+logFile leap.log
+#
+# ----- leaprc for loading the ff14SB force field
+# ----- NOTE: this is designed for PDB format 3!
+#    Uses frcmod.ff14SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA
+#
+#    Uses reduced charges: charged side chains and terminii for proteins
+#       have a net charge of +/- 0.5 (instead of 1); phosphates in nucleic
+#       acids have a net charge of -0.2 (rather than -1)
+#
+#	load atom type hybridizations
+#
+addAtomTypes {
+	{ "H"   "H" "sp3" }
+	{ "HO"  "H" "sp3" }
+	{ "HS"  "H" "sp3" }
+	{ "H1"  "H" "sp3" }
+	{ "H2"  "H" "sp3" }
+	{ "H3"  "H" "sp3" }
+	{ "H4"  "H" "sp3" }
+	{ "H5"  "H" "sp3" }
+	{ "HW"  "H" "sp3" }
+	{ "HC"  "H" "sp3" }
+	{ "HA"  "H" "sp3" }
+	{ "HP"  "H" "sp3" }
+	{ "HZ"  "H" "sp3" }
+	{ "OH"  "O" "sp3" }
+	{ "OS"  "O" "sp3" }
+	{ "O"   "O" "sp2" }
+	{ "O2"  "O" "sp2" }
+	{ "OP"  "O" "sp2" }
+	{ "OW"  "O" "sp3" }
+	{ "CT"  "C" "sp3" }
+	{ "CX"  "C" "sp3" }
+	{ "C8"  "C" "sp3" }
+	{ "2C"  "C" "sp3" }
+	{ "3C"  "C" "sp3" }
+	{ "CH"  "C" "sp3" }
+	{ "CS"  "C" "sp2" }
+	{ "C"   "C" "sp2" }
+	{ "CO"   "C" "sp2" }
+	{ "C*"  "C" "sp2" }
+	{ "CA"  "C" "sp2" }
+	{ "CB"  "C" "sp2" }
+	{ "CC"  "C" "sp2" }
+	{ "CN"  "C" "sp2" }
+	{ "CM"  "C" "sp2" }
+	{ "CK"  "C" "sp2" }
+	{ "CQ"  "C" "sp2" }
+	{ "CD"  "C" "sp2" }
+	{ "C5"  "C" "sp2" }
+	{ "C4"  "C" "sp2" }
+	{ "CP"  "C" "sp2" }
+	{ "CI"  "C" "sp3" }
+	{ "CJ"  "C" "sp2" }
+	{ "CW"  "C" "sp2" }
+	{ "CV"  "C" "sp2" }
+	{ "CR"  "C" "sp2" }
+	{ "CA"  "C" "sp2" }
+	{ "CY"  "C" "sp2" }
+	{ "C0"  "Ca" "sp3" }
+	{ "MG"  "Mg" "sp3" }
+	{ "N"   "N" "sp2" }
+	{ "NA"  "N" "sp2" }
+	{ "N2"  "N" "sp2" }
+	{ "N*"  "N" "sp2" }
+	{ "NP"  "N" "sp2" }
+	{ "NQ"  "N" "sp2" }
+	{ "NB"  "N" "sp2" }
+	{ "NC"  "N" "sp2" }
+	{ "NT"  "N" "sp3" }
+	{ "NY"  "N" "sp2" }
+	{ "N3"  "N" "sp3" }
+	{ "S"   "S" "sp3" }
+	{ "SH"  "S" "sp3" }
+	{ "P"   "P" "sp3" }
+	{ "LP"  ""  "sp3" }
+	{ "EP"  ""  "sp3" }
+	{ "F"   "F" "sp3" }
+	{ "Cl"  "Cl" "sp3" }
+	{ "Br"  "Br" "sp3" }
+	{ "I"   "I"  "sp3" }
+	{ "F-"   "F" "sp3" }
+	{ "Cl-"  "Cl" "sp3" }
+	{ "Br-"  "Br" "sp3" }
+	{ "I-"   "I"  "sp3" }
+	{ "Li+"  "Li"  "sp3" }
+	{ "Na+"  "Na"  "sp3" }
+	{ "K+"  "K"  "sp3" }
+	{ "Rb+"  "Rb"  "sp3" }
+	{ "Cs+"  "Cs"  "sp3" }
+	{ "Mg+"  "Mg"  "sp3" }
+# glycam
+	{ "OG"  "O" "sp3" }
+	{ "OL"  "O" "sp3" }
+	{ "AC"  "C" "sp3" }
+	{ "EC"  "C" "sp3" }
+}
+#
+#	Load the main parameter set.
+#
+parm10 = loadamberparams parm10.dat
+frcmod14SB = loadamberparams frcmod.ff14SB
+#
+#	Load main chain and terminating amino acid libraries, nucleic acids
+#     (reduced charge versions)
+#
+loadOff amino12.redq.lib
+loadOff aminoct12.redq.lib
+loadOff aminont12.redq.lib
+loadOff nucleic12.redq.lib
+#
+#       Load water and ions
+# 
+loadOff atomic_ions.lib
+loadOff solvents.lib
+HOH = TP3
+WAT = TP3
+
+#
+#	Define the PDB name map for the amino acids and nucleic acids
+#
+addPdbResMap {
+  { 0 "HYP" "NHYP" } { 1 "HYP" "CHYP" }
+  { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
+  { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
+  { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
+  { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
+  { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
+  { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
+  { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
+  { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
+  { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
+  { 0 "HID" "NHID" } { 1 "HID" "CHID" }
+  { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
+  { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
+  { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
+  { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
+  { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
+  { 0 "MET" "NMET" } { 1 "MET" "CMET" }
+  { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
+  { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
+  { 0 "SER" "NSER" } { 1 "SER" "CSER" }
+  { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
+  { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
+  { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
+  { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
+  { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
+  { 0 "G" "G5"  } { 1 "G" "G3"  } 
+  { 0 "A" "A5"  } { 1 "A" "A3"  } 
+  { 0 "C" "C5"  } { 1 "C" "C3"  } 
+  { 0 "U" "U5"  } { 1 "U" "U3"  } 
+  { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }  
+  { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }  
+  { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }  
+  { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }  
+#  some old Amber residue names for RNA:
+  { 0  "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" }
+  { 0  "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" }
+  { 0  "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" }
+  { 0  "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" }
+#  some really old Amber residue names, assuming DNA:
+  { 0 "GUA" "DG5"  } { 1 "GUA" "DG3"  } { "GUA" "DG" }
+  { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
+  { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
+  { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
+#  uncomment out the following if you have this old style RNA files:
+# { 0 "GUA" "G5"  } { 1 "GUA" "G3"  } { "GUA" "G" }
+# { 0 "ADE" "A5"  } { 1 "ADE" "A3"  } { "ADE" "A" }
+# { 0 "CYT" "C5"  } { 1 "CYT" "C3"  } { "CYT" "C" }
+# { 0 "URA" "R5"  } { 1 "URA" "R3"  } { "URA" "R" }
+
+}
+
+#  try to be good about reading in really old atom names as well:
+addPdbAtomMap {
+  { "O5*" "O5'" }
+  { "C5*" "C5'" }
+  { "C4*" "C4'" }
+  { "O4*" "O4'" }
+  { "C3*" "C3'" }
+  { "O3*" "O3'" }
+  { "C2*" "C2'" }
+  { "O2*" "O2'" }
+  { "C1*" "C1'" }
+  { "C5M" "C7"  }
+  { "H1*" "H1'" }
+  { "H2*1" "H2'" }
+  { "H2*2" "H2''" }
+  { "H2'1" "H2'" }
+  { "H2'2" "H2''" }
+  { "H3*" "H3'" }
+  { "H4*" "H4'" }
+  { "H5*1" "H5'" }
+  { "H5*2" "H5''" }
+  { "H5'1" "H5'" }
+  { "H5'2" "H5''" }
+  { "HO'2" "HO2'" }
+  { "H5T"  "HO5'" }
+  { "H3T"  "HO3'" }
+  { "O1'" "O4'" }
+  { "OA"  "OP1" }
+  { "OB"  "OP2" }
+  { "O1P" "OP1" }
+  { "O2P" "OP2" }
+}
+
+#
+# assume that most often proteins use HIE
+#
+NHIS = NHIE
+HIS = HIE
+CHIS = CHIE
diff --git a/share/amber/dat/leap/cmd/leaprc.ff14ipq b/share/amber/dat/leap/cmd/leaprc.ff14ipq
@@ -32,15 +32,8 @@ addAtomTypes {
 	{ "OA"  "O"  "sp3" }
 	{ "CT"  "C"  "sp3" }
 	{ "CX"  "C"  "sp3" }
-	{ "TA"  "C"  "sp3" }
-	{ "TD"  "C"  "sp3" }
 	{ "TG"  "C"  "sp3" }
-	{ "TI"  "C"  "sp3" }
-	{ "TL"  "C"  "sp3" }
-	{ "TN"  "C"  "sp3" }
 	{ "TP"  "C"  "sp3" }
-	{ "TS"  "C"  "sp3" }
-	{ "TV"  "C"  "sp3" }
 	{ "C8"  "C"  "sp3" }
 	{ "2C"  "C"  "sp3" }
 	{ "3C"  "C"  "sp3" }
@@ -77,6 +70,7 @@ addAtomTypes {
 	{ "NQ"  "N"  "sp2" }
 	{ "NB"  "N"  "sp2" }
 	{ "NC"  "N"  "sp2" }
+	{ "TN"  "N"  "sp2" }
 	{ "NT"  "N"  "sp3" }
 	{ "NY"  "N"  "sp2" }
 	{ "N3"  "N"  "sp3" }
@@ -178,7 +172,7 @@ addPdbResMap {
 # { 0 "GUA" "G5"  } { 1 "GUA" "G3"  } { "GUA" "G" }
 # { 0 "ADE" "A5"  } { 1 "ADE" "A3"  } { "ADE" "A" }
 # { 0 "CYT" "C5"  } { 1 "CYT" "C3"  } { "CYT" "C" }
-# { 0 "THY" "T5"  } { 1 "THY" "T3"  } { "THY" "T" }
+# { 0 "URA" "R5"  } { 1 "URA" "R3"  } { "URA" "R" }
 
 }
 

diff --git a/share/amber/dat/leap/cmd/leaprc.parmbsc0_chiOL4_ezOL1 b/share/amber/dat/leap/cmd/leaprc.parmbsc0_chiOL4_ezOL1
@@ -0,0 +1,26 @@
+source leaprc.ff14SB 
+
+addAtomTypes {
+	{ "C3"  "C" "sp3" }
+        { "C1"  "C" "sp2" }
+        { "C2"  "C" "sp2" }
+}
+
+addPdbAtomMap {
+  { "H2*1" "H2'1" }
+  { "H2*2" "H2'2" }
+  { "H2'"  "H2'1" }
+  { "H2''" "H2'2" }
+  { "H5'"  "H5'1" }
+  { "H5''" "H5'2" }
+  { "HO2'" "HO'2" }
+  { "HO5'" "H5T" }
+  { "HO3'" "H3T" }
+  { "OP1" "O1P" }
+  { "OP2" "O2P" }
+}
+
+loadamberprep dna_nuc94-bsc0_chiOl4-ezOL1.in
+ez = loadamberparams frcmod.parmbsc0_ezOL1
+chi = loadamberparams frcmod.chiOL4
+
diff --git a/share/amber/dat/leap/cmd/leaprc.phosaa10 b/share/amber/dat/leap/cmd/leaprc.phosaa10
@@ -13,7 +13,7 @@ logFile leap.log
 #
 # To use these residues, load this file into leap, after the Amber-FF, e.g.:
 #
-# > source leaprc.ff12SB
+# > source leaprc.ff14SB
 # > source leaprc.phosaa10
 #
 # The charge model comes from:

diff --git a/share/amber/dat/leap/cmd/leaprc.spce b/share/amber/dat/leap/cmd/leaprc.spce
@@ -0,0 +1,10 @@
+#
+#       Load water and ions for SPC/E + Joung-Chetham monovalent ions
+# 
+loadOff atomic_ions.lib
+loadOff solvents.lib
+HOH = SPC
+WAT = SPC
+loadAmberParams frcmod.spce
+loadAmberParams frcmod.ionsjc_spce
+
diff --git a/share/amber/dat/leap/cmd/leaprc.tip3p b/share/amber/dat/leap/cmd/leaprc.tip3p
@@ -0,0 +1,9 @@
+#
+#       Load water and ions for TIP3P + Joung-Chetham monovalent ions
+# 
+loadOff atomic_ions.lib
+loadOff solvents.lib
+HOH = TP3
+WAT = TP3
+loadAmberParams frcmod.ionsjc_tip3p
+
diff --git a/share/amber/dat/leap/cmd/leaprc.tip4pew b/share/amber/dat/leap/cmd/leaprc.tip4pew
@@ -0,0 +1,10 @@
+#
+#       Load water and ions for TIP4P-ew + Joung-Chetham monovalent ions
+# 
+loadOff atomic_ions.lib
+loadOff solvents.lib
+HOH = T4P
+WAT = T4P
+loadAmberParams frcmod.tip4pew
+loadAmberParams frcmod.ionsjc_tip4pew
+