Merge pull request #477 from marrink-lab/ccap-data

Add charmm data for NCAP and CCAP mappings
marrink-lab · Nov 8, 2022 · 7ca7d6d · 7ca7d6d
2 parents 29bc3d5 + c9ece39
commit 7ca7d6d
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diff --git a/vermouth/data/force_fields/charmm/modifications.ff b/vermouth/data/force_fields/charmm/modifications.ff
@@ -46,6 +46,38 @@ HN2 {"element": "H", "PTM_atom": true, "replace": {"atomname": "HN2"}}
 N CA
 N HN2
 
+[ modification ]
+CCAP-ter
+[ atoms ]
+C {"element": "C"}
+O {"element": "O"}
+OC {"element": "O", "PTM_atom": true}
+CC1 {"element": "C", "PTM_atom": true}
+HCC1 {"element": "H", "PTM_atom": true}
+HCC2 {"element": "H", "PTM_atom": true}
+HCC3 {"element": "H", "PTM_atom": true}
+[ edges ]
+C O
+C OC
+OC CC1
+CC1 HCC1
+CC1 HCC2
+CC1 HCC3
+
+[ modification ]
+NCAP-ter
+[ atoms ]
+N {"element": "N"}
+CC1  {"element": "C", "PTM_atom": true}
+HCC1 {"element": "H", "PTM_atom": true}
+HCC2 {"element": "H", "PTM_atom": true}
+HCC3 {"element": "H", "PTM_atom": true}
+[ edges ]
+N CC1
+CC1 HCC1
+CC1 HCC2
+CC1 HCC3
+
 [ modification ]
 GLU-H
 [ atoms ]

diff --git a/vermouth/data/mappings/martini3001/modifications.charmm36.mapping b/vermouth/data/mappings/martini3001/modifications.charmm36.mapping
@@ -99,3 +99,63 @@ CA  BB
 C   BB
 O   BB
 
+
+[modification]
+[ from ]
+charmm
+[ to ]
+martini3001
+[ from blocks ]
+CCAP-ter
+[ to blocks ]
+CCAP-ter
+[ from nodes ]
+N
+HN
+CA
+[ from edges ]
+HN N
+N CA
+CA C
+[ mapping ]
+HN  BB
+N   BB
+CA  BB
+C   BB
+O   BB
+OC  BB
+CC1 BB
+HCC1 BB
+HCC2 BB
+HCC3 BB
+
+
+[modification]
+[ from ]
+charmm
+[ to ]
+martini3001
+[ from blocks ]
+NCAP-ter
+[ to blocks ]
+NCAP-ter
+[ from nodes ]
+C
+O
+CA
+HN
+[ from edges ]
+C O
+CA C
+CA N
+HN N
+[ mapping ]
+O   BB
+C   BB
+CA  BB
+N   BB
+HN  BB
+CC1 BB
+HCC1 BB
+HCC2 BB
+HCC3 BB