Removed non-ff atomtypes from oplsaa and charmm27

Removed atom types Cu2+, Fe2+ and SI from oplsaa and charmm27,
since they are not part of the official force fields.
Refs #957.

Change-Id: Ic8ebdbee62b4441184a54a580b83849ba21ca978

diff --git a/share/top/charmm27.ff/ffnonbonded.itp b/share/top/charmm27.ff/ffnonbonded.itp
index 82daff23322a6de758854c30aafb31d7b536a25e..34323decbd319e0f477006ad9b1ee996af18f31a 100644 (file)
--- a/share/top/charmm27.ff/ffnonbonded.itp
+++ b/share/top/charmm27.ff/ffnonbonded.itp
@@ -157,11 +157,6 @@ MNH2       0       0.000000        0.00    A       0.0     0.0
 MCH3   0       0.000000        0.00    A       0.0     0.0
 MCH3S  0       0.000000        0.00    A       0.0     0.0
 MW      0       0.000000        0.00    A       0.0     0.0
-; Ions and noble gases (useful for tutorials)
-Cu2+   29      63.54600        2.00    A       2.08470e-01     4.76976e+00
-Ar     18      39.94800        0.00    A       3.41000e-01     2.74580e-02
-; Added by DvdS 05/2005 copied from GROMACS force field.
-SI     14      28.08000        0.00    A       3.38550e-01     2.44704e+00
 
 [ pairtypes ]
 ; i    j       func    sigma1-4        epsilon1-4 ; THESE ARE 1-4 INTERACTIONS

diff --git a/share/top/oplsaa.ff/aminoacids.rtp b/share/top/oplsaa.ff/aminoacids.rtp
index abadb0b3865a2f54bf233617378c95f92d1245fe..07869cb85248ced8548669451473dfe6a92a5a8b 100644 (file)
--- a/share/top/oplsaa.ff/aminoacids.rtp
+++ b/share/top/oplsaa.ff/aminoacids.rtp
@@ -1590,14 +1590,6 @@
  [ atoms ]
     BA   opls_414   2.000     0
 
-; Metal ions 
-[ CU ]
- [ atoms ]
-    CU   Cu2+       2.000     0
-
-[ FE ]
- [ atoms ]
-    FE   Fe2+       2.000     0
 
 ; Ethanol - CA is the carbon bound to the OH group
 [ EtOH ]
@@ -1621,6 +1613,7 @@
    CA    OH
    OH    HO
 
+
 ; New All atom DMSO model, DvdS, 17/06/2006
 ; Use at your own risk!
 [ DMSO  ]

diff --git a/share/top/oplsaa.ff/atomtypes.atp b/share/top/oplsaa.ff/atomtypes.atp
index ce255af96ffa5eba78e52225c563a5b211d539f7..9a5d4a9eed67974e90e4687e6535082a9685b128 100644 (file)
--- a/share/top/oplsaa.ff/atomtypes.atp
+++ b/share/top/oplsaa.ff/atomtypes.atp
@@ -826,12 +826,6 @@
  MCH3B       0.0      ; Dummy mass in rigid tetraedrical CH3 group
  MW          0.0      ; Dummy mass in rigid tyrosine rings
  DUM         0.0      ; Dummy mass in TIP4P etc.
-; These ion atomtypes are NOT part of OPLS, but since they are
-; needed for some proteins we have added them.
- Cu2+       63.546    ; Copper. See Inorg. Chem. 40, 5223 (2001).
- Fe2+       55.847    ; Iron. See Chem. Phys. Lett. 449, 144 (2007).
-; Added by DvdS 05/2005 copied from GROMACS force field.       
- SI         28.080    ; Silicium in Glass etc.
 ; tip4p-EW
 HW_tip4pew   1.008 
 OW_tip4pew   16.00 

diff --git a/share/top/oplsaa.ff/ffbonded.itp b/share/top/oplsaa.ff/ffbonded.itp
index 357af4d8fd84e8aac0f15008cf67b2ec56de908a..907840488f15cae12e9de5cf3e326ad626ce00be 100644 (file)
--- a/share/top/oplsaa.ff/ffbonded.itp
+++ b/share/top/oplsaa.ff/ffbonded.itp
@@ -2666,28 +2666,6 @@
 #define improper_Z_CA_X_Y       180.0      4.60240   2
 
 
-; 
-; This bit added by DvdS for quartz simulation 2005-05-07
-; These parameters are taken from GROMOS and were also used in
-; Wensink et al. Langmuir 16 (2000) pp. 7392-7400
-;
-[ bondtypes ]
-; i    j  func       b0          kb
-  SI    OS      1    0.16300     251040.  ; From GROMACS
-  SI    OH      1    0.16300     251040.  ;
-  
-[ angletypes ]
-;  i    j    k  func       th0       cth
-   SI   OS   SI    1   155.000     397.480
-   OS   SI   OS    1   109.500     397.480
-   OH   SI   OS    1   109.500     397.480
-   SI   OH   HO    1   109.500     397.480
-   
-[ dihedraltypes ]
-;  i    j    k    l   func     coefficients
-; Added DvdS for Quartz simulations
-   SI   OS    1     0.000       3.766      3
-   SI   OH    1     0.000       3.766      3
 
 ; Added by DvdS for DMSO 17/06/2006
  [ bondtypes ]

diff --git a/share/top/oplsaa.ff/ffnonbonded.itp b/share/top/oplsaa.ff/ffnonbonded.itp
index 6887f656eeed7a6412076e2b50e9d1e8cddfe8df..20e5b31d9562f4c368c3b9ece318ed5892712e5b 100644 (file)
--- a/share/top/oplsaa.ff/ffnonbonded.itp
+++ b/share/top/oplsaa.ff/ffnonbonded.itp
@@ -823,12 +823,6 @@
  MCH3A      MCH3A   0  0.00000     0.000       A    0.00000e+00  0.00000e+00
  MCH3B      MCH3B   0  0.00000     0.000       A    0.00000e+00  0.00000e+00
  MW         MW      0  0.00000     0.000       D    0.00000e+00  0.00000e+00
-; These ion atomtypes are NOT part of OPLS, but since they are
-; needed for some proteins.
- Cu2+       Cu2+   29  63.54600     2.000       A    2.08470e-01  4.76976e+00
- Fe2+       Fe2+   26  55.84700     2.000       A    2.59400e-01  5.43920e-02
-; Added by DvdS 05/2005 copied from GROMACS force field.       
- SI         SI     14  28.08000     0.000       A    3.38550e-01  2.44704e+00
 ; tip4p-EW
 HW_tip4pew   1       1.008   0.0000  A   0.00000e+00  0.00000e+00
 OW_tip4pew   8      16.00    0.0000  A   3.16435e-01  6.80946e-01

diff --git a/share/top/oplsaa.ff/ions.itp b/share/top/oplsaa.ff/ions.itp
index 83c21cac87fe8a1aead6269664fffeaa413a2497..b60240da7de17a4385e047da51846e7fca9f5b99 100644 (file)
--- a/share/top/oplsaa.ff/ions.itp
+++ b/share/top/oplsaa.ff/ions.itp
@@ -2,14 +2,6 @@
 ; See literature references in forcefield.itp and atomtypes.atp
 ;
 
-[ moleculetype ]
-; molname   nrexcl
-CU          1
-
-[ atoms ]
-; id    at type res nr  residu name at name  cg nr  charge   mass
-1       Cu2+    1       CU          CU       1      2        63.54600
-
 [ moleculetype ]
 ; molname   nrexcl
 MG          1