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

diff --git a/share/top/charmm27.ff/aminoacids.c.tdb b/share/top/charmm27.ff/aminoacids.c.tdb
index 884cb95bfd2eb0b7e76670e0ee38a2508e71d968..a83083643cbb92799558fc352eb1b76608903309 100644 (file)
--- a/share/top/charmm27.ff/aminoacids.c.tdb
+++ b/share/top/charmm27.ff/aminoacids.c.tdb
@@ -7,7 +7,7 @@
  OXT   OT2     OC              15.9994 -0.67   
 [ add ]
  2     8       OT      C       CA      N
-       OC      15.9994 -0.67
+       OC      15.9994 -0.67   -1
 [ impropers ]
  C     CA      OT2     OT1      
 
@@ -19,9 +19,9 @@
  OXT   OT2     OH              15.9994 -0.61
 [ add ]
  2     8       OT      C       CA      N
-       OB      15.9994 -0.55
+       OB      15.9994 -0.55   -1
  1     2       HT2     OT2     C       CA
-       H       1.008   0.44
+       H       1.008   0.44    -1
 [ replace ]
  OT2   OT2     OH1             15.9994 -0.61
 [ impropers ]
@@ -34,9 +34,9 @@
  O             O               15.9994 -0.55
 [ add ]
  1     2       NT      C       CA      N
-       NH2     14.0027 -0.62
+       NH2     14.0027 -0.62   -1
  2     3       HT      NT      C       CA
-       H       1.008   0.00
+       H       1.008   0.00    -1
 [ replace ]
  HT1           H               1.008   0.30    ; this one is trans to O
  HT2           H               1.008   0.32    ; this one is cis to O
@@ -61,13 +61,13 @@
 OXT
 [ add ]
 1      8       NT       C      CA      N
-        NH1    14.0027  -0.47
+        NH1    14.0027  -0.47  -1
 1      2       HNT      NT     C       O
-        H       1.008   0.31
+        H       1.008   0.31   -1
 1      8       CAT      NT     C       O
-        CT3   12.011  -0.11
+        CT3   12.011  -0.11    -1
 3      4       HT       CAT    NT      C
-        HA      1.008   0.09
+        HA      1.008   0.09   -1
 [ bonds ]
 NT    CAT              ; otherwise CAT does not get bonded to other atoms...
 [ impropers ]

diff --git a/share/top/charmm27.ff/aminoacids.n.tdb b/share/top/charmm27.ff/aminoacids.n.tdb
index 5c35c3a875eb1f1a48267e33834af57deff2bec9..53fc89d5034a747aec39c5e01d28bb69f5841a8e 100644 (file)
--- a/share/top/charmm27.ff/aminoacids.n.tdb
+++ b/share/top/charmm27.ff/aminoacids.n.tdb
@@ -6,7 +6,7 @@
  CA    CA      CT2             12.011  0.13
 [ Add ]
  3     4       H       N       CA      C
-       HC      1.008   0.33
+       HC      1.008   0.33    -1
 [ delete ]
  HN
 
@@ -17,7 +17,7 @@
  HA      HA    HB              1.008    0.10
 [ Add ]
  3       4       H       N       CA      C
-         HC      1.008   0.33
+         HC      1.008   0.33   -1
 [ delete ]
  HN
 
@@ -28,7 +28,7 @@
  CD      CD    CP3      12.011  0.16
 [ add ]
  2       4       H       N       CA      C
-        HC      1.008   0.24
+        HC      1.008   0.24    -1
 
 ; 
 [ NH2 ]
@@ -38,7 +38,7 @@
  HA            HB              1.008   0.09
 [ add ]
  2     4       HT      N       CA      C
-       H       1.008   0.34
+       H       1.008   0.34    -1
 [ delete ]
  HN
 
@@ -50,7 +50,7 @@
  CA            CT2             12.011  0.10
 [ add ]
  2     4       HT      N       CA      C
-       H       1.008   0.34
+       H       1.008   0.34    -1
 [ delete ]
  HN
 
@@ -63,7 +63,7 @@
  CD            CP3     12.011  -0.10
 [ add ]
  1     4       H       N       CA      C
- HC    1.008   0.31
+       HC      1.008   0.31    -1
 
 
 

diff --git a/share/top/charmm27.ff/aminoacids.r2b b/share/top/charmm27.ff/aminoacids.r2b
index 9296d0194d9bb9d011ba1b0e0eed5584ac66f729..41bcbab9f1415cf2f0c653c0537854c0583ba5ec 100644 (file)
--- a/share/top/charmm27.ff/aminoacids.r2b
+++ b/share/top/charmm27.ff/aminoacids.r2b
@@ -6,4 +6,4 @@ HISH    HSP
 LYSN   LSN
 ASPH   ASPP
 GLUH   GLUP
-HEM     HEME
+HEM    HEME

diff --git a/share/top/charmm27.ff/aminoacids.rtp b/share/top/charmm27.ff/aminoacids.rtp
index 904612cdc8c69d8846048b063fdcebb2d5412385..f9f68238a417db3208e2c85cb261236741008f22 100644 (file)
--- a/share/top/charmm27.ff/aminoacids.rtp
+++ b/share/top/charmm27.ff/aminoacids.rtp
@@ -175,18 +175,18 @@
 [ ASPP ] ; protonated ASP
  [ atoms ]
         N       NH1     -0.47   0
-        HN      H       0.31    0
-        CA      CT1     0.07    0
-        HA      HB      0.09    0
-        CB      CT2    -0.21    1 ;
-        HB1     HA      0.09    1 ; HB1    OD1
-        HB2     HA      0.09    1 ;  |    //
-        CG      CD      0.75    1 ; -CB--CG
-        OD1     OB     -0.55    1 ;  |     \
-        OD2     OH1    -0.61    1 ; HB2     OD2-HD2
-        HD2     H       0.44    1 ;
-        C       C       0.51    2
-        O       O       -0.51   2
+        HN      H       0.31    1
+        CA      CT1     0.07    2
+        HA      HB      0.09    3
+        CB      CT2    -0.21    4 ;
+        HB1     HA      0.09    5 ; HB1    OD1
+        HB2     HA      0.09    6 ;  |    //
+        CG      CD      0.75    7 ; -CB--CG
+        OD1     OB     -0.55    8 ;  |     \
+        OD2     OH1    -0.61    9 ; HB2     OD2-HD2
+        HD2     H       0.44    10;
+        C       C       0.51    11
+        O       O       -0.51   12
  [ bonds ]
         CB      CA
         CG      CB
@@ -242,15 +242,15 @@
 [ CYS2 ]  ; disulfide cystine
  [ atoms ]
         N       NH1     -0.47   0
-        HN      H       0.31    0
-        CA      CT1     0.07    0
-        HA      HB      0.09    0
-        CB      CT2     -0.10   1
-        HB1     HA      0.09    1
-        HB2     HA      0.09    1
-        SG      SM      -0.08   1
-        C       C       0.51    2
-        O       O       -0.51   2
+        HN      H       0.31    1
+        CA      CT1     0.07    2
+        HA      HB      0.09    3
+        CB      CT2     -0.10   4
+        HB1     HA      0.09    5
+        HB2     HA      0.09    6
+        SG      SM      -0.08   7
+        C       C       0.51    8
+        O       O       -0.51   9
  [ bonds ]
         CB      CA
         SG      CB
@@ -358,21 +358,21 @@
 [ GLUP ] ; protonated GLU
  [ atoms ]
         N       NH1     -0.47   0
-        HN      H       0.31    0
-        CA      CT1     0.07    0
-        HA      HB      0.09    0
-        CB      CT2     -0.18   1
-        HB1     HA      0.09    1
-        HB2     HA      0.09    1
-        CG      CT2    -0.21    2 ;
-        HG1     HA      0.09    2 ; HG1    OE1
-        HG2     HA      0.09    2 ;  |    //
-        CD      CD      0.75    2 ; -CG--CD
-        OE1     OB     -0.55    2 ;  |     \
-        OE2     OH1    -0.61    2 ; HG2     OE2-HE2
-        HE2     H       0.44    2 ;
-        C       C       0.51    3
-        O       O       -0.51   3
+        HN      H       0.31    1
+        CA      CT1     0.07    2
+        HA      HB      0.09    3
+        CB      CT2     -0.18   4
+        HB1     HA      0.09    5
+        HB2     HA      0.09    6
+        CG      CT2    -0.21    7 ;
+        HG1     HA      0.09    8 ; HG1    OE1
+        HG2     HA      0.09    9 ;  |    //
+        CD      CD      0.75    10; -CG--CD
+        OE1     OB     -0.55    11;  |     \
+        OE2     OH1    -0.61    12; HG2     OE2-HE2
+        HE2     H       0.44    13;
+        C       C       0.51    14
+        O       O       -0.51   15
  [ bonds ]
         CB      CA
         CG      CB
@@ -720,26 +720,26 @@
 [ LSN ] ; neutral lysine residue
  [ atoms ]
         N       NH1     -0.47   0
-        HN      H       0.31    0
-        CA      CT1     0.07    0
-        HA      HB      0.09    0
-        CB      CT2     -0.18   1
-        HB1     HA      0.09    1
-        HB2     HA      0.09    1
-        CG      CT2     -0.18   2
-        HG1     HA      0.09    2
-        HG2     HA      0.09    2
-        CD      CT2     -0.18   3
-        HD1     HA      0.09    3
-        HD2     HA      0.09    3
-        CE      CT2     0.13    4
-        HE1     HA      0.075   4
-        HE2     HA      0.075   4
-        NZ      NH2     -0.96   4
-        HZ1     HC      0.34    4
-        HZ2     HC      0.34    4
-        C       C       0.51    5
-        O       O       -0.51   5
+        HN      H       0.31    1
+        CA      CT1     0.07    2
+        HA      HB      0.09    3
+        CB      CT2     -0.18   4
+        HB1     HA      0.09    5
+        HB2     HA      0.09    6
+        CG      CT2     -0.18   7
+        HG1     HA      0.09    8
+        HG2     HA      0.09    9
+        CD      CT2     -0.18   10
+        HD1     HA      0.09    11
+        HD2     HA      0.09    12
+        CE      CT2     0.13    13
+        HE1     HA      0.075   14
+        HE2     HA      0.075   15
+        NZ      NH2     -0.96   16
+        HZ1     HC      0.34    17
+        HZ2     HC      0.34    18
+        C       C       0.51    19
+        O       O       -0.51   20
  [ bonds ]
         CB      CA
         CG      CB
@@ -1176,78 +1176,78 @@
 [ HEME ]
  [ atoms ]
        FE      FE       0.24   0
-       NA      NPH     -0.18   0
-       NB      NPH     -0.18   0
-       NC      NPH     -0.18   0
-       ND      NPH     -0.18   0
-       C1A     CPA      0.12   0
-       C2A     CPB     -0.06   0
-       C3A     CPB     -0.06   0
-       C4A     CPA      0.12   0
-       C1B     CPA      0.12   0
-       C2B     CPB     -0.06   0
-       C3B     CPB     -0.06   0
-       C4B     CPA      0.12   0
-       C1C     CPA      0.12   0
-       C2C     CPB     -0.06   0
-       C3C     CPB     -0.06   0
-       C4C     CPA      0.12   0
-       C1D     CPA      0.12   0
-       C2D     CPB     -0.06   0
-       C3D     CPB     -0.06   0
-       C4D     CPA      0.12   0
-       CHA     CPM     -0.10   1
-       HA      HA       0.10   1
-       CHB     CPM     -0.10   2
-       HB      HA       0.10   2
-       CHC     CPM     -0.10   3
-       HC      HA       0.10   3
-       CHD     CPM     -0.10   4
-       HD      HA       0.10   4
-       CMA     CT3     -0.27   5
-       HMA1    HA       0.09   5
-       HMA2    HA       0.09   5
-       HMA3    HA       0.09   5
-       CAA     CT2     -0.18   6
-       HAA1    HA       0.09   6
-       HAA2    HA       0.09   6
-       CBA     CT2     -0.28   7
-       HBA1    HA       0.09   7
-       HBA2    HA       0.09   7
-       CGA     CC       0.62   7
-       O1A     OC      -0.76   7
-       O2A     OC      -0.76   7
-       CMB     CT3     -0.27   8
-       HMB1    HA       0.09   8
-       HMB2    HA       0.09   8
-       HMB3    HA       0.09   8
-       CAB     CE1     -0.15   9
-       HAB     HE1      0.15   9
-       CBB     CE2     -0.42   10
-       HBB1    HE2      0.21   10
-       HBB2    HE2      0.21   10
-       CMC     CT3     -0.27   11
-       HMC1    HA       0.09   11
-       HMC2    HA       0.09   11
-       HMC3    HA       0.09   11
-       CAC     CE1     -0.15   12
-       HAC     HE1      0.15   12
-       CBC     CE2     -0.42   13
-       HBC1    HE2      0.21   13
-       HBC2    HE2      0.21   13
-       CMD     CT3     -0.27   14
-       HMD1    HA       0.09   14
-       HMD2    HA       0.09   14
-       HMD3    HA       0.09   14
-       CAD     CT2     -0.18   15
-       HAD1    HA       0.09   15
-       HAD2    HA       0.09   15
-       CBD     CT2     -0.28   16
-       HBD1    HA       0.09   16
-       HBD2    HA       0.09   16
-       CGD     CC       0.62   16
-       O1D     OC      -0.76   16
-       O2D     OC      -0.76   16
+       NA      NPH     -0.18   1
+       NB      NPH     -0.18   2
+       NC      NPH     -0.18   3
+       ND      NPH     -0.18   4
+       C1A     CPA      0.12   5
+       C2A     CPB     -0.06   6
+       C3A     CPB     -0.06   7
+       C4A     CPA      0.12   8
+       C1B     CPA      0.12   9
+       C2B     CPB     -0.06   10
+       C3B     CPB     -0.06   11
+       C4B     CPA      0.12   12
+       C1C     CPA      0.12   13
+       C2C     CPB     -0.06   14
+       C3C     CPB     -0.06   15
+       C4C     CPA      0.12   16
+       C1D     CPA      0.12   17
+       C2D     CPB     -0.06   18
+       C3D     CPB     -0.06   19
+       C4D     CPA      0.12   20
+       CHA     CPM     -0.10   21
+       HA      HA       0.10   22
+       CHB     CPM     -0.10   23
+       HB      HA       0.10   24
+       CHC     CPM     -0.10   25
+       HC      HA       0.10   26
+       CHD     CPM     -0.10   27
+       HD      HA       0.10   28
+       CMA     CT3     -0.27   29
+       HMA1    HA       0.09   30
+       HMA2    HA       0.09   31
+       HMA3    HA       0.09   32
+       CAA     CT2     -0.18   33
+       HAA1    HA       0.09   34
+       HAA2    HA       0.09   35
+       CBA     CT2     -0.28   36
+       HBA1    HA       0.09   37
+       HBA2    HA       0.09   38
+       CGA     CC       0.62   39
+       O1A     OC      -0.76   40
+       O2A     OC      -0.76   41
+       CMB     CT3     -0.27   42
+       HMB1    HA       0.09   43
+       HMB2    HA       0.09   44
+       HMB3    HA       0.09   45
+       CAB     CE1     -0.15   46
+       HAB     HE1      0.15   47
+       CBB     CE2     -0.42   48
+       HBB1    HE2      0.21   49
+       HBB2    HE2      0.21   50
+       CMC     CT3     -0.27   51
+       HMC1    HA       0.09   52
+       HMC2    HA       0.09   53
+       HMC3    HA       0.09   54
+       CAC     CE1     -0.15   55
+       HAC     HE1      0.15   56
+       CBC     CE2     -0.42   57
+       HBC1    HE2      0.21   58
+       HBC2    HE2      0.21   59
+       CMD     CT3     -0.27   60
+       HMD1    HA       0.09   61
+       HMD2    HA       0.09   62
+       HMD3    HA       0.09   63
+       CAD     CT2     -0.18   64
+       HAD1    HA       0.09   65
+       HAD2    HA       0.09   66
+       CBD     CT2     -0.28   67
+       HBD1    HA       0.09   68
+       HBD2    HA       0.09   69
+       CGD     CC       0.62   70
+       O1D     OC      -0.76   71
+       O2D     OC      -0.76   72
  [ bonds ]
        FE      NA
        FE      NB
@@ -1388,80 +1388,80 @@
 [ HEO2 ]
  [ atoms ]
        FE      FE       0.24   0
-       NA      NPH     -0.18   0
-       NB      NPH     -0.18   0
-       NC      NPH     -0.18   0
-       ND      NPH     -0.18   0
-       C1A     CPA      0.12   0
-       C2A     CPB     -0.06   0
-       C3A     CPB     -0.06   0
-       C4A     CPA      0.12   0
-       C1B     CPA      0.12   0
-       C2B     CPB     -0.06   0
-       C3B     CPB     -0.06   0
-       C4B     CPA      0.12   0
-       C1C     CPA      0.12   0
-       C2C     CPB     -0.06   0
-       C3C     CPB     -0.06   0
-       C4C     CPA      0.12   0
-       C1D     CPA      0.12   0
-       C2D     CPB     -0.06   0
-       C3D     CPB     -0.06   0
-       C4D     CPA      0.12   0
-       CHA     CPM     -0.10   1
-       HA      HA       0.10   1
-       CHB     CPM     -0.10   2
-       HB      HA       0.10   2
-       CHC     CPM     -0.10   3
-       HC      HA       0.10   3
-       CHD     CPM     -0.10   4
-       HD      HA       0.10   4
-       CMA     CT3     -0.27   5
-       HMA1    HA       0.09   5
-       HMA2    HA       0.09   5
-       HMA3    HA       0.09   5
-       CAA     CT2     -0.18   6
-       HAA1    HA       0.09   6
-       HAA2    HA       0.09   6
-       CBA     CT2     -0.28   7
-       HBA1    HA       0.09   7
-       HBA2    HA       0.09   7
-       CGA     CC       0.62   7
-       O1A     OC      -0.76   7
-       O2A     OC      -0.76   7
-       CMB     CT3     -0.27   8
-       HMB1    HA       0.09   8
-       HMB2    HA       0.09   8
-       HMB3    HA       0.09   8
-       CAB     CE1     -0.15   9
-       HAB     HE1      0.15   9
-       CBB     CE2     -0.42   10
-       HBB1    HE2      0.21   10
-       HBB2    HE2      0.21   10
-       CMC     CT3     -0.27   11
-       HMC1    HA       0.09   11
-       HMC2    HA       0.09   11
-       HMC3    HA       0.09   11
-       CAC     CE1     -0.15   12
-       HAC     HE1      0.15   12
-       CBC     CE2     -0.42   13
-       HBC1    HE2      0.21   13
-       HBC2    HE2      0.21   13
-       CMD     CT3     -0.27   14
-       HMD1    HA       0.09   14
-       HMD2    HA       0.09   14
-       HMD3    HA       0.09   14
-       CAD     CT2     -0.18   15
-       HAD1    HA       0.09   15
-       HAD2    HA       0.09   15
-       CBD     CT2     -0.28   16
-       HBD1    HA       0.09   16
-       HBD2    HA       0.09   16
-       CGD     CC       0.62   16
-       O1D     OC      -0.76   16
-       O2D     OC      -0.76   16
-       O1      OM      0.021   17
-       O2      OM     -0.021   17
+       NA      NPH     -0.18   1
+       NB      NPH     -0.18   2
+       NC      NPH     -0.18   3
+       ND      NPH     -0.18   4
+       C1A     CPA      0.12   5
+       C2A     CPB     -0.06   6
+       C3A     CPB     -0.06   7
+       C4A     CPA      0.12   8
+       C1B     CPA      0.12   9
+       C2B     CPB     -0.06   10
+       C3B     CPB     -0.06   11
+       C4B     CPA      0.12   12
+       C1C     CPA      0.12   13
+       C2C     CPB     -0.06   14
+       C3C     CPB     -0.06   15
+       C4C     CPA      0.12   16
+       C1D     CPA      0.12   17
+       C2D     CPB     -0.06   18
+       C3D     CPB     -0.06   19
+       C4D     CPA      0.12   20
+       CHA     CPM     -0.10   21
+       HA      HA       0.10   22
+       CHB     CPM     -0.10   23
+       HB      HA       0.10   24
+       CHC     CPM     -0.10   25
+       HC      HA       0.10   26
+       CHD     CPM     -0.10   27
+       HD      HA       0.10   28
+       CMA     CT3     -0.27   29
+       HMA1    HA       0.09   30
+       HMA2    HA       0.09   31
+       HMA3    HA       0.09   32
+       CAA     CT2     -0.18   33
+       HAA1    HA       0.09   34
+       HAA2    HA       0.09   35
+       CBA     CT2     -0.28   36
+       HBA1    HA       0.09   37
+       HBA2    HA       0.09   38
+       CGA     CC       0.62   39
+       O1A     OC      -0.76   40
+       O2A     OC      -0.76   41
+       CMB     CT3     -0.27   42
+       HMB1    HA       0.09   43
+       HMB2    HA       0.09   44
+       HMB3    HA       0.09   45
+       CAB     CE1     -0.15   46
+       HAB     HE1      0.15   47
+       CBB     CE2     -0.42   48
+       HBB1    HE2      0.21   49
+       HBB2    HE2      0.21   50
+       CMC     CT3     -0.27   51
+       HMC1    HA       0.09   52
+       HMC2    HA       0.09   53
+       HMC3    HA       0.09   54
+       CAC     CE1     -0.15   55
+       HAC     HE1      0.15   56
+       CBC     CE2     -0.42   57
+       HBC1    HE2      0.21   58
+       HBC2    HE2      0.21   59
+       CMD     CT3     -0.27   60
+       HMD1    HA       0.09   61
+       HMD2    HA       0.09   62
+       HMD3    HA       0.09   63
+       CAD     CT2     -0.18   64
+       HAD1    HA       0.09   65
+       HAD2    HA       0.09   66
+       CBD     CT2     -0.28   67
+       HBD1    HA       0.09   68
+       HBD2    HA       0.09   69
+       CGD     CC       0.62   70
+       O1D     OC      -0.76   71
+       O2D     OC      -0.76   72
+       O1      OM      0.021   73
+       O2      OM     -0.021   74
  [ bonds ]
        FE      NA
        FE      NB
@@ -1605,22 +1605,22 @@
 [ O2 ] ; O2 ligand for HEME
  [ atoms ]
        O1      OM      0.021   0
-       O2      OM     -0.021   0
+       O2      OM     -0.021   1
  [ bonds ]
        O1 O2
 
 [ CO ] ; CO ligand for HEME
  [ atoms ]
        C       CM      0.021   0
-       O       OM     -0.021   0
+       O       OM     -0.021   1
  [ bonds ]
        C O
 
 [ HOH ]
  [ atoms ]
         OW      OT      -0.834  0
-        HW1     HT      0.417   0
-        HW2     HT      0.417   0
+        HW1     HT      0.417   1
+        HW2     HT      0.417   2
  [ bonds ]
         OW      HW1
         OW      HW2

diff --git a/share/top/charmm27.ff/dna.r2b b/share/top/charmm27.ff/dna.r2b
new file mode 100644 (file)
index 0000000..e7bed5d
--- /dev/null
+++ b/share/top/charmm27.ff/dna.r2b
@@ -0,0 +1,7 @@
+; rtp residue to rtp building block table
+;GMX   Force-field
+A    DA
+G    DG
+C    DC
+T    DT
+

diff --git a/share/top/charmm27.ff/dna.rtp b/share/top/charmm27.ff/dna.rtp
index 485ea0182d202fe88d61938281bcbb52bcb1aa25..72bd8df318994f77e0e6c3f1b30337f653abc171 100644 (file)
--- a/share/top/charmm27.ff/dna.rtp
+++ b/share/top/charmm27.ff/dna.rtp
@@ -403,3 +403,4 @@ C2  N1      N3      O2
 C4     N3      C5      O4
 C5     C4      C6      C5M
 
+

diff --git a/share/top/charmm27.ff/forcefield.doc b/share/top/charmm27.ff/forcefield.doc
index eac68cb7cd33d1d1b27af503feaa3da70c5d0c1d..47eec6cec7118649ab8ce98c01c9af6e839ec4e2 100644 (file)
--- a/share/top/charmm27.ff/forcefield.doc
+++ b/share/top/charmm27.ff/forcefield.doc
@@ -1,4 +1,4 @@
-CHARMM27 all-atom force field (with CMAP) - version 2.0beta
+CHARMM27 all-atom force field (with CMAP) - version 2.0
 
 *******************************************************************************
 *                    CHARMM port writted by                                   *

diff --git a/share/top/charmm27.ff/rna.r2b b/share/top/charmm27.ff/rna.r2b
index d30b5290fedcffc4252305621bfd3c3d75a34a51..0f69cb469ccb9be079d2443b9cb543291d9b304b 100644 (file)
--- a/share/top/charmm27.ff/rna.r2b
+++ b/share/top/charmm27.ff/rna.r2b
@@ -1,6 +1,6 @@
 ; rtp residue to rtp building block table
 ;GMX   Force-field
-A     RA
-G     RG
-C     RC
-U     RU
+A     RA       
+G     RG       
+C     RC       
+U     RU       

diff --git a/share/top/charmm27.ff/rna.rtp b/share/top/charmm27.ff/rna.rtp
index 3abc189d2a173b16f7aaf05f595456dd68362019..78d01d6ee5882c0bbe8f46344d93033a1b087cea 100644 (file)
--- a/share/top/charmm27.ff/rna.rtp
+++ b/share/top/charmm27.ff/rna.rtp
@@ -403,4 +403,5 @@ C5  C6
 [ impropers ]
 C2     N1      N3      O2
 C4     N3      C5      O4
+ 
 

diff --git a/src/kernel/pdb2top.c b/src/kernel/pdb2top.c
index bc03decca477ca7a0f35808d68dbb096ce756a08..1384f0a8555c70146d246b16b44a52497951f270 100644 (file)
--- a/src/kernel/pdb2top.c
+++ b/src/kernel/pdb2top.c
@@ -476,8 +476,12 @@ static int name2type(t_atoms *at, int **cgnr, gpp_atomtype_t atype,
       at->atom[i].m    = get_atomtype_massA(restp[resind].atom[j].type,
                                            atype);
       cg = restp[resind].cgnr[j];
-      if ( (cg != prevcg) || (resind != prevresind) )
-       curcg++;
+      /* A charge group number -1 signals a separate charge group
+       * for this atom.
+       */
+      if ( (cg == -1) || (cg != prevcg) || (resind != prevresind) ) {
+          curcg++;
+      }
     } else {
       if (debug)
        fprintf(debug,"atom %d%s: curcg=%d, qt=%g, is_int=%d\n",

diff --git a/src/kernel/runner.c b/src/kernel/runner.c
index fd0953c4229f3ae3be79df7c1b250a38ee9d48d0..557a467a473e8d80ff900716d7fae205ea32461f 100644 (file)
--- a/src/kernel/runner.c
+++ b/src/kernel/runner.c
@@ -446,6 +446,12 @@ int mdrunner(int nthreads_requested, FILE *fplog,t_commrec *cr,int nfile,
             );
     }
 
+    if ((Flags & MD_RERUN) &&
+        (EI_ENERGY_MINIMIZATION(inputrec->eI) || eiNM == inputrec->eI))
+    {
+        gmx_fatal(FARGS, "The .mdp file specified an energy mininization or normal mode algorithm, and these are not compatible with mdrun -rerun");
+    }
+
     if (can_use_allvsall(inputrec,mtop,TRUE,cr,fplog))
     {
         /* All-vs-all loops do not work with domain decomposition */

diff --git a/src/tools/gmx_sas.c b/src/tools/gmx_sas.c
index 573e3968a12c93d186a2196b079dec00e5803b48..cb6ac71c58a6d2ee33abef77376a2b78ba6a2ef3 100644 (file)
--- a/src/tools/gmx_sas.c
+++ b/src/tools/gmx_sas.c
@@ -226,6 +226,7 @@ void sas_plot(int nfile,t_filenm fnm[],real solsize,int ndots,
   const char   *flegend[] = { "Hydrophobic", "Hydrophilic", 
                              "Total", "D Gsolv" };
   const char   *vlegend[] = { "Volume (nm\\S3\\N)", "Density (g/l)" };
+  const char   *or_and_oa_legend[] = { "Average (nm\\S2\\N)", "Standard deviation (nm\\S2\\N)" };
   const char   *vfile;
   real         t;
   gmx_atomprop_t aps=NULL;
@@ -499,10 +500,12 @@ void sas_plot(int nfile,t_filenm fnm[],real solsize,int ndots,
       atom_area2[i] /= nfr;
     }
     fprintf(stderr,"Printing out areas per atom\n");
-    fp  = xvgropen(opt2fn("-or",nfile,fnm),"Area per residue","Residue",
+    fp  = xvgropen(opt2fn("-or",nfile,fnm),"Area per residue over the trajectory","Residue",
                   "Area (nm\\S2\\N)",oenv);
-    fp2 = xvgropen(opt2fn("-oa",nfile,fnm),"Area per atom","Atom #",
+    xvgr_legend(fp, asize(or_and_oa_legend),or_and_oa_legend,oenv);
+    fp2 = xvgropen(opt2fn("-oa",nfile,fnm),"Area per atom over the trajectory","Atom #",
                   "Area (nm\\S2\\N)",oenv);
+    xvgr_legend(fp2, asize(or_and_oa_legend),or_and_oa_legend,oenv);
     if (bITP) {
       fp3 = ftp2FILE(efITP,nfile,fnm,"w");
       fprintf(fp3,"[ position_restraints ]\n"
@@ -570,7 +573,7 @@ int gmx_sas(int argc,char *argv[])
     "and a group for the output. The calculation group should always",
     "consists of all the non-solvent atoms in the system.",
     "The output group can be the whole or part of the calculation group.",
-    "The area can be plotted",
+    "The average and standard deviation of the area over the trajectory can be plotted",
     "per residue and atom as well (options [TT]-or[tt] and [TT]-oa[tt]).",
     "In combination with the latter option an [TT]itp[tt] file can be",
     "generated (option [TT]-i[tt])",