Merge branch 'release-4-5-patches' into release-4-6

[alexxy/gromacs.git] / share / top / charmm27.ff / aminoacids.rtp

diff --git a/share/top/charmm27.ff/aminoacids.rtp b/share/top/charmm27.ff/aminoacids.rtp
index f3e84ae860bc4e5286a762ad06c5dd5d23de5b73..d24ef05e5173956f03aa56c6cba390f58c9a9345 100644 (file)
--- a/share/top/charmm27.ff/aminoacids.rtp
+++ b/share/top/charmm27.ff/aminoacids.rtp
@@ -1,14 +1,26 @@
 [ bondedtypes ] 
-; Col 1: Type of bond 
-; Col 2: Type of angles 
-; Col 3: Type of proper dihedrals 
-; Col 4: Type of improper dihedrals 
-; Col 5: Generate all dihedrals if 1, only heavy atoms of 0. 
-; Col 6: Number of excluded neighbors for nonbonded interactions 
-; Col 7: Generate 1,4 interactions between pairs of hydrogens if 1 
-; Col 8: Remove propers over the same bond as an improper if it is 1 
-; bonds  angles  dihedrals  impropers all_dihedrals nrexcl HH14 RemoveDih 
-     1       5          9        2        1           3      1     0 
+; Column 1 : default bondtype
+; Column 2 : default angletype
+; Column 3 : default proper dihedraltype
+; Column 4 : default improper dihedraltype
+; Column 5 : This controls the generation of dihedrals from the bonding.
+;            All possible dihedrals are generated automatically. A value of
+;            1 here means that all these are retained. A value of
+;            0 here requires generated dihedrals be removed if
+;              * there are any dihedrals on the same central atoms
+;                specified in the residue topology, or
+;              * there are other identical generated dihedrals
+;                sharing the same central atoms, or
+;              * there are other generated dihedrals sharing the
+;                same central bond that have fewer hydrogen atoms
+; Column 6 : number of neighbors to exclude from non-bonded interactions
+; Column 7 : 1 = generate 1,4 interactions between pairs of hydrogen atoms
+;            0 = do not generate such
+; Column 8 : 1 = remove proper dihedrals if found centered on the same
+;                bond as an improper dihedral
+;            0 = do not generate such
+; bondtype angletype dihedraltype impropertype all_dih nrexcl HH14 bRemoveDih
+     1       5            9            2         1       3     1       0
 
 [ ALA ]
  [ atoms ]