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Merge pull request #138 from marrink-lab/update-m3
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Include all the hydrogens to the martini3 mappings
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@pckroon
pckroon committed Oct 1, 2018
2 parents c2e0172 + f3a78a5 commit 3330397
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Showing 20 changed files with 127 additions and 63 deletions.
4 changes: 4 additions & 0 deletions vermouth/data/mappings/martini30/ala.charmm36.map
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Expand Up @@ -31,7 +31,11 @@ charmm27 charmm36
1 N BB
2 HN BB
3 CA BB
4 HA !BB
5 CB BB
6 HB1 !BB
7 HB2 !BB
8 HB3 !BB
9 C BB
10 O BB

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7 changes: 7 additions & 0 deletions vermouth/data/mappings/martini30/arg.charmm36.map
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Expand Up @@ -31,9 +31,16 @@ charmm27 charmm36
1 N BB
2 HN BB
3 CA BB
4 HA !BB
5 CB SC1
6 HB1 !SC1
7 HB2 !SC1
8 CG SC1
9 HG1 !SC1
10 HG2 !SC1
11 CD SC1
12 HD1 !SC1
13 HD2 !SC1
14 NE SC2
15 HE SC2
16 CZ SC2
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6 changes: 3 additions & 3 deletions vermouth/data/mappings/martini30/asn.charmm36.map
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Expand Up @@ -31,10 +31,10 @@ charmm27 charmm36
1 N BB
2 HN BB
3 CA BB
; 4 HA BB
4 HA !BB
5 CB SC1
; 6 HB1 SC1
; 7 HB2 SC1
6 HB1 !SC1
7 HB2 !SC1
8 CG SC1
9 OD1 SC1
10 ND2 SC1
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8 changes: 4 additions & 4 deletions vermouth/data/mappings/martini30/asp.charmm36.map
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Expand Up @@ -31,14 +31,14 @@ charmm27 charmm36
1 N BB
2 HN BB
3 CA BB
; 4 HA BB
4 HA !BB
5 CB SC1
; 6 HB1 SC1
; 7 HB2 SC1
6 HB1 !SC1
7 HB2 !SC1
8 CG SC1
9 OD1 SC1
10 OD2 SC1
; 11 HD2 SC1
11 HD2 !SC1
12 C BB
13 O BB

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12 changes: 8 additions & 4 deletions vermouth/data/mappings/martini30/cys.charmm36.map
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Expand Up @@ -31,10 +31,14 @@ charmm27 charmm36
1 N BB
2 HN BB
3 CA BB
4 CB SC1
7 SG SC1
9 C BB
10 O BB
4 HA !BB
5 CB SC1
6 HB1 !SC1
7 HB2 !SC1
8 SG SC1
9 HG1 !SC1
10 C BB
11 O BB

[ chiral ]
CB CA N C
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27 changes: 16 additions & 11 deletions vermouth/data/mappings/martini30/gln.charmm36.map
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Expand Up @@ -31,17 +31,22 @@ charmm27 charmm36
1 N BB
2 HN BB
3 CA BB
4 CB SC1
5 CG SC1
6 CD SC1
7 OE1 SC1
8 NE2 SC1
9 HE21 SC1
10 HE22 SC1
11 HE11 SC1
12 HE12 SC1
13 C BB
14 O BB
4 HA !BB
5 CB SC1
6 HB1 !SC1
7 HB2 !SC1
8 CG SC1
9 HG1 !SC1
10 HG2 !SC1
11 CD SC1
12 OE1 SC1
13 NE2 SC1
14 HE21 SC1
15 HE22 SC1
16 HE11 SC1
17 HE12 SC1
18 C BB
19 O BB

[ chiral ]
CB CA N C
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12 changes: 6 additions & 6 deletions vermouth/data/mappings/martini30/glu.charmm36.map
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Expand Up @@ -31,17 +31,17 @@ charmm27 charmm36
1 N BB
2 HN BB
3 CA BB
; 4 HA BB
4 HA !BB
5 CB SC1
; 6 HB1 SC1
; 7 HB2 SC1
6 HB1 !SC1
7 HB2 !SC1
8 CG SC1
; 9 HG1 SC1
; 10 HG2 SC1
9 HG1 !SC1
10 HG2 !SC1
11 CD SC1
12 OE1 SC1
13 OE2 SC1
; 14 HE2 SC1
14 HE2 !SC1
15 C BB
16 O BB

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2 changes: 2 additions & 0 deletions vermouth/data/mappings/martini30/gly.charmm36.map
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Expand Up @@ -31,5 +31,7 @@ charmm27 charmm36
1 N BB
2 HN BB
3 CA BB
4 HA1 !BB
5 HA2 !BB
9 C BB
10 O BB
3 changes: 3 additions & 0 deletions vermouth/data/mappings/martini30/his.charmm36.map
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Expand Up @@ -31,7 +31,10 @@ charmm27 charmm36
1 N BB
2 HN BB
3 CA BB
4 HA !BB
5 CB SC1
6 HB1 !SC1
7 HB2 !SC1
8 CD2 SC2
9 HD2 SC2
10 CG SC1
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20 changes: 10 additions & 10 deletions vermouth/data/mappings/martini30/ile.charmm36.map
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Expand Up @@ -31,20 +31,20 @@ charmm27 charmm36
1 N BB
2 HN BB
3 CA BB
; 4 HA BB
4 HA !BB
5 CB SC1
; 6 HB SC1
6 HB !SC1
7 CG2 SC1
; 8 HG21 SC1
; 9 HG22 SC1
; 10 HG23 SC1
8 HG21 !SC1
9 HG22 !SC1
10 HG23 !SC1
11 CG1 SC1
; 12 HG11 SC1
; 13 HG12 SC1
12 HG11 !SC1
13 HG12 !SC1
14 CD SC1
; 15 HD1 SC1
; 16 HD2 SC1
; 17 HD3 SC1
15 HD1 !SC1
16 HD2 !SC1
17 HD3 !SC1
18 C BB
19 O BB

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10 changes: 10 additions & 0 deletions vermouth/data/mappings/martini30/leu.charmm36.map
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Original file line number Diff line number Diff line change
Expand Up @@ -31,10 +31,20 @@ charmm27 charmm36
1 N BB
2 HN BB
3 CA BB
4 HA !BB
5 CB SC1
6 HB1 !SC1
7 HB2 !SC1
8 CG SC1
9 HG !SC1
10 CD1 SC1
11 HD11 !SC1
12 HD12 !SC1
13 HD13 !SC1
14 CD2 SC1
15 HD21 !SC1
16 HD22 !SC1
17 HD23 !SC1
18 C BB
19 O BB

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18 changes: 9 additions & 9 deletions vermouth/data/mappings/martini30/lys.charmm36.map
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Expand Up @@ -31,19 +31,19 @@ charmm27 charmm36
1 N BB
2 HN BB
3 CA BB
; 4 HA BB
4 HA !BB
5 CB SC1
; 6 HB1 SC1
; 7 HB2 SC1
6 HB1 !SC1
7 HB2 !SC1
8 CG SC1
; 9 HG1 SC1
; 10 HG2 SC1
9 HG1 !SC1
10 HG2 !SC1
11 CD SC1
; 12 HD1 SC1
; 13 HD2 SC1
12 HD1 !SC1
13 HD2 !SC1
14 CE SC2
; 15 HE1 SC2
; 16 HE2 SC2
15 HE1 !SC2
16 HE2 !SC2
17 NZ SC2
18 HZ1 SC2
19 HZ2 SC2
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16 changes: 8 additions & 8 deletions vermouth/data/mappings/martini30/met.charmm36.map
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Expand Up @@ -31,18 +31,18 @@ charmm27 charmm36
1 N BB
2 HN BB
3 CA BB
; 4 HA BB
4 HA !BB
5 CB SC1
; 6 HB1 SC1
; 7 HB2 SC1
6 HB1 !SC1
7 HB2 !SC1
8 CG SC1
; 9 HG1 SC1
; 10 HG2 SC1
9 HG1 !SC1
10 HG2 !SC1
11 SD SC1
12 CE SC1
; 13 HE1 SC1
; 14 HE2 SC1
; 15 HE3 SC1
13 HE1 !SC1
14 HE2 !SC1
15 HE3 !SC1
16 C BB
17 O BB

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6 changes: 3 additions & 3 deletions vermouth/data/mappings/martini30/phe.charmm36.map
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Original file line number Diff line number Diff line change
Expand Up @@ -31,10 +31,10 @@ charmm27 charmm36
1 N BB
2 HN BB
3 CA BB
; 4 HA BB
4 HA !BB
5 CB SC1
; 6 HB1 SC1
; 7 HB2 SC1
6 HB1 !SC1
7 HB2 !SC1
8 CG SC1
9 CD1 SC1
10 HD1 SC1
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17 changes: 12 additions & 5 deletions vermouth/data/mappings/martini30/pro.charmm36.map
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Expand Up @@ -30,11 +30,18 @@ charmm27 charmm36
[ atoms ]
1 N BB
2 CD SC1
3 CA BB
4 CB SC1
5 CG SC1
6 C BB
7 O BB
3 HD1 !SC1
4 HD2 !SC1
5 CA BB
6 HA !BB
7 CB SC1
8 HB1 !SC1
9 HB2 !SC1
10 CG SC1
11 HG1 !SC1
12 HG2 !SC1
13 C BB
14 O BB

[ chiral ]
CB CA N C
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3 changes: 3 additions & 0 deletions vermouth/data/mappings/martini30/ser.charmm36.map
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,10 @@ charmm27 charmm36
1 N BB
2 HN BB
3 CA BB
4 HA !BB
5 CB SC1
6 HB1 !SC1
7 HB2 !SC1
8 OG SC1
9 HG1 SC1
10 C BB
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5 changes: 5 additions & 0 deletions vermouth/data/mappings/martini30/thr.charmm36.map
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Original file line number Diff line number Diff line change
Expand Up @@ -31,10 +31,15 @@ charmm27 charmm36
1 N BB
2 HN BB
3 CA BB
4 HA !BB
5 CB SC1
6 HB !SC1
7 OG1 SC1
8 HG1 SC1
9 CG2 SC1
10 HG21 !SC1
11 HG22 !SC1
11 HG23 !SC1
13 C BB
14 O BB

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3 changes: 3 additions & 0 deletions vermouth/data/mappings/martini30/trp.charmm36.map
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,10 @@ charmm27 charmm36
1 N BB
2 HN BB
3 CA BB
4 HA !BB
5 CB SC1
6 HB1 !SC1
7 HB2 !SC2
8 CG SC1
9 CD1 SC2
10 HD1 SC2
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3 changes: 3 additions & 0 deletions vermouth/data/mappings/martini30/tyr.charmm36.map
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,10 @@ charmm27 charmm36
1 N BB
2 HN BB
3 CA BB
4 HA !BB
5 CB SC1
6 HB1 !SC1
7 HB2 !SC1
8 CG SC1
9 CD1 SC2
10 HD1 SC2
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8 changes: 8 additions & 0 deletions vermouth/data/mappings/martini30/val.charmm36.map
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Original file line number Diff line number Diff line change
Expand Up @@ -31,9 +31,17 @@ charmm27 charmm36
1 N BB
2 HN BB
3 CA BB
4 HA !BB
5 CB SC1
6 HB !SC1
8 CG1 SC1
9 HG11 !SC1
10 HG12 !SC1
11 HG13 !SC1
12 CG2 SC1
13 HG21 !SC1
14 HG22 !SC1
15 HG23 !SC1
16 C BB
17 O BB

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