Merge branch 'master' into DNA-exten/itp

marrink-lab · Apr 5, 2022 · b12036f · b12036f
2 parents ac0685e + 1d42c30
commit b12036f
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Showing 22 changed files with 797 additions and 420 deletions.
diff --git a/polyply/data/2016H66/polyether_blocks.ff b/polyply/data/2016H66/polyether_blocks.ff
@@ -13,3 +13,18 @@ PEO 3
 3 2 2 gb_18 {"comment":"CHn-OA,OE"}
 [ angles ]
 3 2 1 2 ga_15 {"comment":"CHn-CHn-C,CHn,OA,OE,NR,NT,NL"}
+
+; this residue is exclusively intended to be a side-chain
+; substiuent to PMA or PMMA. It is identical in all other
+; ways to PEO
+[ moleculetype ]
+mPEG 3
+[ atoms ]
+1 CH3 1 mPEG EC1 1 0.29 15.0350
+2 OE  1 mPEG O1 2 -0.58 15.9994
+3 CH3 1 mPEG EC2 3 0.29 15.0350
+[ bonds ]
+1 2 2 gb_18 {"comment":"CHn-OA,OE"}
+3 2 2 gb_18 {"comment":"CHn-OA,OE"}
+[ angles ]
+3 2 1 2 ga_15 {"comment":"CHn-CHn-C,CHn,OA,OE,NR,NT,NL"}
diff --git a/polyply/data/2016H66/polyether_links.ff b/polyply/data/2016H66/polyether_links.ff
@@ -2,7 +2,7 @@
 ;  POLYETHER-BONDS
 ;---------------------------
 [ link ]
-resname "PEO"
+resname "PEO|mPEG"
 [ atoms ]
 EC2 {"replace": {"atype": "CH2", "mass": "14.0270"}}
 +EC1 {"replace": {"atype": "CH2", "mass": "14.0270"}}
@@ -13,33 +13,33 @@ EC2 {"replace": {"atype": "CH2", "mass": "14.0270"}}
 ;  POLYETHER-ANGLES
 ;---------------------------
 [ link ]
-resname "PEO"
+resname "PEO|mPEG"
 [ angles ]
 EC2 +EC1 +O1 2 ga_15 {"comment":"CHn-CHn-C,CHn,OA,OE,NR,NT,NL", "group":"link"}
 [ link ]
-resname "PEO"
+resname "PEO|mPEG"
 [ angles ]
 +EC1 EC2 O1 2 ga_15 {"comment":"CHn-CHn-C,CHn,OA,OE,NR,NT,NL", "group":"link"}
 
 ;---------------------------
 ;  POLYETHER-DIHEDRALS
 ;---------------------------
 [ link ]
-resname "PEO"
+resname "PEO|mPEG"
 [ dihedrals ]
 EC1 O1 EC2 +EC1 1 gd_42 {"comment":"CHn-CHn-OE-CHn", "version":"1" , "group":"link"}
 EC1 O1 EC2 +EC1 1 gd_43 {"comment":"CHn-CHn-OE-CHn", "version":"2" , "group":"link"}
 EC1 O1 EC2 +EC1 1 gd_44 {"comment":"CHn-CHn-OE-CHn", "version":"3" , "group":"link"}
 
 [ link ]
-resname "PEO"
+resname "PEO|mPEG"
 [ dihedrals ]
 O1 EC2 +EC1 +O1 1 gd_45 {"comment":"OE-CHn-CHn-OE", "version":"1" , "group":"link"}
 O1 EC2 +EC1 +O1 1 gd_46 {"comment":"OE-CHn-CHn-OE", "version":"2" , "group":"link"}
 O1 EC2 +EC1 +O1 1 gd_47 {"comment":"OE-CHn-CHn-OE", "version":"3" , "group":"link"}
 
 [ link ]
-resname "PEO"
+resname "PEO|mPEG"
 [ dihedrals ]
 EC2 +EC1 +O1 +EC2 1 gd_42 {"comment":"CHn-CHn-OE-CHn", "version":"1" , "group":"link"}
 EC2 +EC1 +O1 +EC2 1 gd_43 {"comment":"CHn-CHn-OE-CHn", "version":"2" , "group":"link"}
@@ -49,7 +49,7 @@ EC2 +EC1 +O1 +EC2 1 gd_44 {"comment":"CHn-CHn-OE-CHn", "version":"3" , "group":"
 ;  POLYETHER-PAIRS
 ;---------------------------
 [ link ]
-resname "PEO"
+resname "PEO|mPEG"
 [ atoms ]
 EC1 { }
 O1 { }
@@ -83,7 +83,7 @@ EC2 +EC1
 +EC1 +O1
 +O1 +EC2
 [ link ]
-resname "PEO"
+resname "PEO|mPEG"
 [ atoms ]
 EC1 { }
 O1 { }

diff --git a/polyply/data/2016H66/polyether_polyvinyl_links.ff b/polyply/data/2016H66/polyether_polyvinyl_links.ff
@@ -1,6 +1,9 @@
+[ macros ]
+PEO_VINYL_RES "PEO|PE|PMMA|PMA|PP|PVA|PS|HEA|PAM|PMAM"
+
 [ link ]
 ; ether -> vinyl
-resname "PEO|PE|PMA|PP|PVA|PS|HEA"
+resname $PEO_VINYL_RES
 [ atoms ]
 EC1 { }
 O1 { }
@@ -28,7 +31,7 @@ EC2 +VC1
 
 [ link ]
 ; vinyl -> ether
-resname "PEO|PE|PMA|PP|PVA|PS|HEA"
+resname $PEO_VINYL_RES
 [ atoms ]
 VC1 { }
 VC2 {"replace":{"atype": "CH2", "mass": "14.0270"}}
@@ -56,7 +59,7 @@ VC2 +EC1
 
 [ link ]
 ; side chain substiuent vinyl -> ether
-resname "PEO|PMA|PP|PVA|PS|HEA"
+resname $PEO_VINYL_RES
 [ atoms ]
 VC1 { }
 VC2 { }
@@ -67,17 +70,17 @@ SC3 { }
 [ angles ]
 SC3 VC1 +EC1 ga_15 {"comment":"CHn-CHn-C,CHn,OA,OE,NR,NT,NL", "group":"link"}
 [ pairs ]
-SC3 +O1 { "group": "link" }
+SC3 +O1 1 { "group": "link" }
 [ edges ]
 VC1 VC2
 VC2 SC3
 VC2 +EC1
 +EC1 +O1
 +EC1 +EC2
-
+;
 [ link ]
 ; side chain substiuent ether -> vinyl
-resname "PEO|PMA|PP|PVA|PS|HEA"
+resname $PEO_VINYL_RES
 [ atoms ]
 EC1 { }
 O1 { }
@@ -86,7 +89,7 @@ EC2 { }
 +VC2 { }
 +SC3 { }
 [ pairs ]
-EC2 +SC3 { "group": "link" }
+EC2 +SC3 1 { "group": "link" }
 [ edges ]
 EC1 O1
 O1 EC2
@@ -95,7 +98,7 @@ EC2 +VC1
 +VC2 +SC3
 
 [ link ]
-resname "PEO|PE|PMA|PP|PVA|PS|HEA"
+resname $PEO_VINYL_RES
 ; vinyl -> vinyl -> ether
 [ atoms ]
 VC1 { }
@@ -117,7 +120,7 @@ VC2 +VC1
 ++O1 ++EC2
 
 [ link ]
-resname "PEO|PE|PMA|PP|PVA|PS|HEA"
+resname $PEO_VINYL_RES
 ; ether  -> vinyl -> vinyl
 [ atoms ]
 EC1  { }
@@ -128,7 +131,7 @@ EC2 { }
 ++VC1 { }
 ++VC2 { }
 [ pairs ]
-EC2 ++VC1
+EC2 ++VC1 1
 [ dihedrals ]
 EC2 +VC1 +VC2 ++VC1 1 gd_34 {"comment":"X-SI,CHn-CHn-X", "group":"link"}
 [ edges ]
@@ -140,13 +143,13 @@ EC2 +VC1
 ++VC1 ++VC2
 
 [ link ]
-resname "PEO|PE|PMA|PP|PVA|PS|HEA"
+resname $PEO_VINYL_RES
 ; ether -> vinyl -> ether
 [ atoms ]
 EC1 { }
 O1 { }
 EC2 { }
-"PEO|PE|PMA|PP|PVA|PS"+VC1 { }
++VC1 { }
 +VC2 { }
 ++EC1 { }
 ++O1 { }
@@ -164,49 +167,41 @@ EC2 +VC1
 ++EC1 ++O1
 ++O1 ++EC2
 
-;[ link ]
-; ether -> vinyl <- ether
-;[ pairs ]
-;EC2 +EC2
-;[ dihedrals ]
-;EC2 ++VC1 ++VC2 +EC2 1 gd_34 {"comment":"X-SI,CHn-CHn-X", "group":"link"}
-;[ edges ]
-;EC1 O1
-;O1 EC2
-;EC2 ++VC1
-;++VC1 ++VC2
-;++VC2 +EC2
-;+EC2 +O1
-;+O1 +EC1
-
-;[ link ]
-; ether <- vinyl -> ether
-;[ pairs ]
-;+EC1 ++EC1
-;[ dihedrals ]
-;+EC1 VC1 VC2 ++EC2 1 gd_34 {"comment":"X-SI,CHn-CHn-X", "group":"link"}
-;[ edges ]
-;+EC1 +O1
-;+O1 +EC2
-;+EC2 VC1
-;VC1 VC2
-;VC2 ++EC2
-;++EC2 ++O1
-;++O1 ++EC1
-
-;[ link ]
-; ether <- vinyl <- ether
-;[ pairs ]
-;EC2 ++EC1
-;[ dihedrals ]
-;EC2 +VC2 +VC1 +EC1 1 gd_34 {"comment":"X-SI,CHn-CHn-X", "group":"link"}
-;[ edges ]
-;EC1 O1
-;O1 EC2
-;EC2 ++VC1
-;++VC1 ++VC2
-;++VC2 +EC2
-;+EC2 +O1
-;+O1 +EC1
-
-
+[ link ]
+; mPEG PMMA/PMA
+resname "mPEG|PMA|PMMA"
+[ atoms ]
+SC1 { }
+SC2 { }
+SC3 { }
+SC4 {"replace":{"atype": "CH2", "mass": "14.0270"} }
+>EC1 {"replace":{"atype": "CH2", "mass": "14.0270"} }
+>O1 { }
+>EC2 { }
+[ bonds  ]
+SC4 >EC1 2 gb_27 {"comment":"C,CHn-CHn,C", "group":"link"}
+[ angles ]
+SC3 SC4 >EC1 2 ga_15 {"comment":"CHn-CHn-C,CHn,OA,OE,NR,NT,NL", "group":"link"}
+SC4 >EC1 >O1 2 ga_15 {"comment":"CHn-CHn-C,CHn,OA,OE,NR,NT,NL", "group":"link"}
+[ dihedrals ]
+; C-O-C-C
+SC1 SC3 SC4 >EC1 1 gd_42 {"comment":"CHn-CHn-OE-CHn", "version":"1" , "group":"link"}
+SC1 SC3 SC4 >EC1 1 gd_43 {"comment":"CHn-CHn-OE-CHn", "version":"2" , "group":"link"}
+SC1 SC3 SC4 >EC1 1 gd_44 {"comment":"CHn-CHn-OE-CHn", "version":"3" , "group":"link"}
+; O-C-C-O
+SC3 SC4 >EC1 >O1 1 gd_45 {"comment":"OE-CHn-CHn-OE", "version":"1" , "group":"link"}
+SC3 SC4 >EC1 >O1 1 gd_46 {"comment":"OE-CHn-CHn-OE", "version":"2" , "group":"link"}
+SC3 SC4 >EC1 >O1 1 gd_47 {"comment":"OE-CHn-CHn-OE", "version":"3" , "group":"link"}
+; C-C-O-C
+SC4 >EC1 >O1 >EC2 1 gd_42 {"comment":"CHn-CHn-OE-CHn", "version":"1" , "group":"link"}
+SC4 >EC1 >O1 >EC2 1 gd_43 {"comment":"CHn-CHn-OE-CHn", "version":"2" , "group":"link"}
+SC4 >EC1 >O1 >EC2 1 gd_44 {"comment":"CHn-CHn-OE-CHn", "version":"3" , "group":"link"}
+[ pairs ]
+SC1  >EC1 1 { "group": "link" }
+SC3  >O1  1 { "group": "link" }
+SC4   >EC2 1 { "group": "link" }
+[ edges ]
+SC1 SC3
+SC3 SC4
+SC4 >EC1
+>EC1 >O1