Remove ff19ipq (#419)

amber/biopolymer.yaml

@@ -34,15 +34,6 @@
     J. Chem. Theory Comput., 2016, 12, 3926-3947.
   Test:
   - protein
-- Source: files/ff19ipq/leaprc.protein.ff19ipq
-  Prefix: protein
-  Reference:
-  - >-
-    Debiec, K.T.; Cerutti, D.S.; Baker, L.R.; Gronenborn, A.M.; Case, D.A.; Chong, L.T.
-    Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model.
-    J. Chem. Theory Comput., 2016, 12, 3926-3947.
-  Test:
-  - protein
 - Source: oldff/leaprc.lipid17
   CharmmFFXMLFilename: ../openmmforcefields/ffxml/charmm/charmm36_nowaters.xml
   CharmmLipid2AmberFilename: files/charmmlipid2amber.csv

amber/files/ff19ipq/README

@@ -1,4 +0,0 @@
-The parm19ipq.dat is missing a newline between the end of the nonbonded
-parameters and END, and ParmEd won't read it, so the files are copied with an
-extra line added to parm19ipq.dat and the leaprc modified to point to the
-modified parm19ipq.dat.

amber/files/ff19ipq/leaprc.protein.ff19ipq

@@ -1,160 +0,0 @@
-logFile leap.log
-#
-# ----- leaprc for loading the ff15ipq force field, developmental version
-# ----- NOTE: this is designed for PDB format 3!
-#       Version 10.3, solvated:
-#         Charges fit with H sigma=1.3 and SPC/Eb, backbone charges held equal
-#        
-#         vdw (LJEDITs removed, H sigma=1.3, ARG side chain TH sigma=1.5)
-#         torsions generation 6 (0 ff14ipq, ALAPROALA,
-#                                1 dipeptides,
-#                                2 XXXGLY & GLYXXX tripeptides,
-#                                3 XXXPRO & PROXXX tripeptides)
-#                                4 charged tripeptides)
-#                                5 more charged tripeptides and termini
-#                                6 angle peptides and more termini)
-#         Parm cleaned up extensively
-#         Torsion phases restored to 0 and 180 degrees
-#         Backbone CNA, HNA, NAC, ACN, and ACO angles fit
-#         Additional assorted updates to bonded parameters and types
-#         The SPC/Eb water model was used to derive partial charges
-#           for this force field
-#
-#	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" }
-	{ "TH"  "H"  "sp3" }
-	{ "OH"  "O"  "sp3" }
-	{ "OS"  "O"  "sp3" }
-	{ "O"   "O"  "sp2" }
-	{ "OD"  "O"  "sp2" }
-	{ "O2"  "O"  "sp2" }
-	{ "O3"  "O"  "sp2" }
-	{ "OP"  "O"  "sp2" }
-	{ "OW"  "O"  "sp3" }
-	{ "OA"  "O"  "sp3" }
-	{ "CT"  "C"  "sp3" }
-	{ "CX"  "C"  "sp3" }
-	{ "TJ"  "C"  "sp3" }
-	{ "TG"  "C"  "sp3" }
-	{ "TM"  "C"  "sp3" }
-	{ "TP"  "C"  "sp3" }
-	{ "C8"  "C"  "sp3" }
-	{ "2C"  "C"  "sp3" }
-	{ "3C"  "C"  "sp3" }
-	{ "TA"  "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" }
-	{ "TN"  "N"  "sp2" }
-	{ "NT"  "N"  "sp3" }
-	{ "NY"  "N"  "sp2" }
-	{ "N3"  "N"  "sp3" }
-	{ "NL"  "N"  "sp3" }
-	{ "ND"  "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" }
-}
-#
-#	Load the main parameter set.
-#
-parm19ipq = loadAmberParams files/ff19ipq/parm19ipq.dat
-#
-#       Load main chain and terminating amino acid libraries, nucleic acids
-#
-loadOff amino19ipq_0.9.lib
-loadOff aminoct19ipq_0.9.lib
-loadOff aminont19ipq_0.9.lib
-
-#
-#	Define the PDB name map for the amino acids 
-#
-addPdbResMap {
-  { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
-  { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
-  { 0 "ASH" "NASH" } { 1 "ASH" "CASH" }
-  { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
-  { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
-  { 0 "CYM" "NCYM" } { 1 "CYM" "CCYM" }
-  { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
-  { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
-  { 0 "GLH" "NGLH" } { 1 "GLH" "CGLH" }
-  { 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" }
-                     { 1 "LYN" "CLYN" }
-  { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
-  { 0 "MET" "NMET" } { 1 "MET" "CMET" }
-  { 0 "NLE" "NNLE" } { 1 "NLE" "CNLE" }
-  { 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" }
-
-}
-
-#
-# assume that most often proteins use HIE
-#
-NHIS = NHIE
-HIS = HIE
-CHIS = CHIE