Merge pull request #427 from marrink-lab/fix/425

Fix/425
marrink-lab · Jun 23, 2022 · 16de64e · 16de64e
2 parents 69fe046 + 3355a9f
commit 16de64e
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diff --git a/doc/source/conf.py b/doc/source/conf.py
@@ -71,7 +71,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = 'en'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.

diff --git a/...h/data/force_fields/elnedyn/aminoacids.ff → ...data/force_fields/elnedyn21/aminoacids.ff b/...h/data/force_fields/elnedyn/aminoacids.ff → ...data/force_fields/elnedyn21/aminoacids.ff
@@ -140,7 +140,7 @@ PRO                1
 [ atoms ]
 ;id type resnr residu atom cgnr   charge
  1   Na   1     PRO     BB     1      0    
- 2   C2   1     PRO     SC1    2      0    
+ 2  AC2   1     PRO     SC1    2      0    
 
 [constraints]
 #meta {"group": "Side chain bonds"}

diff --git a/...h/data/force_fields/elnedyn/citations.bib → ...data/force_fields/elnedyn21/citations.bib b/...h/data/force_fields/elnedyn/citations.bib → ...data/force_fields/elnedyn21/citations.bib
diff --git a/...outh/data/force_fields/elnedyn/general.ff → ...th/data/force_fields/elnedyn21/general.ff b/...outh/data/force_fields/elnedyn/general.ff → ...th/data/force_fields/elnedyn21/general.ff
diff --git a/...ata/force_fields/elnedyn/modifications.ff → ...a/force_fields/elnedyn21/modifications.ff b/...ata/force_fields/elnedyn/modifications.ff → ...a/force_fields/elnedyn21/modifications.ff
diff --git a/vermouth/data/force_fields/elnedyn22p/aminoacids.ff b/vermouth/data/force_fields/elnedyn22p/aminoacids.ff
@@ -75,7 +75,7 @@ VAL                1
 [ atoms ]
 ;id type resnr residu atom cgnr   charge
  1   P5   1     VAL     BB     1      0    
- 2   AC2  1     VAL     SC1    2      0    
+ 2   C2  1     VAL     SC1    2      0    
 
 [constraints]
 ;  i     j   funct   length  
@@ -91,7 +91,7 @@ LEU                1
 [ atoms ]
 ;id type resnr residu atom cgnr   charge
  1   P5   1     LEU     BB     1      0    
- 2   AC1  1     LEU     SC1    2      0    
+ 2   C1  1     LEU     SC1    2      0    
 
 [constraints]
 #meta {"group": "Side chain bonds"}
@@ -108,7 +108,7 @@ ILE                1
 [ atoms ]
 ;id type resnr residu atom cgnr   charge
  1   P5   1     ILE     BB     1      0    
- 2   AC1  1     ILE     SC1    2      0    
+ 2   C1  1     ILE     SC1    2      0    
 
 [bonds]
 #meta {"group": "Side chain bonds"}
@@ -159,13 +159,26 @@ ASN                1
 [ atoms ]
 ;id type resnr residu atom cgnr   charge
  1   P5    1     ASN     BB     1      0    
- 2   P5    1     ASN     SC1    2      0    
+ 2   Nda   1     ASN     SC1    2      0    
+ 3   D     1     ASN     SCP    3  +0.46  36 {"charge_dummy": 0.14}
+ 4   D     1     ASN     SCN    4  -0.46  36 {"charge_dummy": 0.14}
+
+[virtual_sites2]
+; Site from       funct a
+   2     3    4   1     0.5
+
+[ edges ]
+SCP SC1
+SCN SC1
 
 [ constraints ]
 #meta {"group": "Side chain bonds"}
 ;  i     j   funct   length
    1     2    1       0.250
 
+[constraints]
+;  i     j   funct   length
+   3     4    1       0.28
 
 ;;; GLUTAMINE
 
@@ -280,7 +293,7 @@ THR                1
 [ atoms ]
 ;id type resnr residu atom cgnr   charge
 1   P5     1     THR     BB     1      0    
-2   P1     1     THR     SC1    2      0     0
+2   N0     1     THR     SC1    2      0     0
 3   D      1     THR     SCP    3  +0.36    36 {"charge_dummy": 0.14}
 4   D      1     THR     SCN    4  -0.36    36 {"charge_dummy": 0.14}
 

diff --git a/vermouth/data/mappings/elnedyn/ala.charmm36.map b/vermouth/data/mappings/elnedyn/ala.charmm36.map
@@ -19,7 +19,7 @@ ALA
 universal
 
 [to]
-elnedyn
+elnedyn21
 elnedyn22
 elnedyn22p
 

diff --git a/vermouth/data/mappings/elnedyn/arg.charmm36.map b/vermouth/data/mappings/elnedyn/arg.charmm36.map
@@ -19,7 +19,7 @@ ARG
 universal
 
 [to]
-elnedyn
+elnedyn21
 elnedyn22
 
 [ martini ]

diff --git a/vermouth/data/mappings/elnedyn/asn.charmm36.map b/vermouth/data/mappings/elnedyn/asn.charmm36.map
@@ -19,7 +19,7 @@ ASN
 universal
 
 [to]
-elnedyn
+elnedyn21
 elnedyn22
 
 [ martini ]

diff --git a/vermouth/data/mappings/elnedyn/asp.charmm36.map b/vermouth/data/mappings/elnedyn/asp.charmm36.map
@@ -19,7 +19,7 @@ ASP
 universal
 
 [to]
-elnedyn
+elnedyn21
 elnedyn22
 
 [ martini ]

diff --git a/vermouth/data/mappings/elnedyn/chol.charmm36.map b/vermouth/data/mappings/elnedyn/chol.charmm36.map
diff --git a/vermouth/data/mappings/elnedyn/cys.charmm36.map b/vermouth/data/mappings/elnedyn/cys.charmm36.map
@@ -19,7 +19,7 @@ CYS
 universal
 
 [to]
-elnedyn
+elnedyn21
 elnedyn22
 elnedyn22p