Merge "Remove rest of the xml support" into release-4-6

diff --git a/share/top/oplsaa.ff/aminoacids.rtp b/share/top/oplsaa.ff/aminoacids.rtp
index fd21b48467f18cfc7ee593c113dfad5e5735b1e2..597e3eb9a4afae11ceaeed611f5ee0b58316468f 100644 (file)
--- a/share/top/oplsaa.ff/aminoacids.rtp
+++ b/share/top/oplsaa.ff/aminoacids.rtp
@@ -1599,16 +1599,6 @@
  [ atoms ]
     FE   Fe2+       2.000     0
 
-[ ZN ]
- [ atoms ]
-    ZN   Zn2+       2.000     0
-
-; And argon...
-[ Ar ]
- [ atoms ]
-    Ar     Ar       0.000     0
-
-
 ; Ethanol - CA is the carbon bound to the OH group
 [ EtOH ]
  [ atoms ]

diff --git a/share/top/oplsaa.ff/atomtypes.atp b/share/top/oplsaa.ff/atomtypes.atp
index 304c21563d2609bc128d96774ee9ca82d812018e..5dbc1a89bce67ba081647ca88dbd62a88143f866 100644 (file)
--- a/share/top/oplsaa.ff/atomtypes.atp
+++ b/share/top/oplsaa.ff/atomtypes.atp
@@ -829,8 +829,6 @@
 ; 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 
- Zn2+       65.370    ; Zinc 
- Ar         39.948    ; Argon
+ 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.

diff --git a/share/top/oplsaa.ff/ffnonbonded.itp b/share/top/oplsaa.ff/ffnonbonded.itp
index c8659d3246231c7ed07de3b14f1c35bea13f2cc0..124b1de91ba457d201cb5bea717582558b595bfb 100644 (file)
--- a/share/top/oplsaa.ff/ffnonbonded.itp
+++ b/share/top/oplsaa.ff/ffnonbonded.itp
@@ -823,10 +823,8 @@
  MCH3B      MCH3B   0  0.00000     0.000       A    0.00000e+00  0.00000e+00
  MW         MW      0  0.00000     0.000       A    0.00000e+00  0.00000e+00
 ; These ion atomtypes are NOT part of OPLS, but since they are
-; needed for some proteins or tutorial Argon simulations we have added them.
+; 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
- Zn2+       Zn2+   30  65.37000     2.000       A    1.95200e-01  9.78219e-01
- Ar         Ar     18  39.94800     0.000       A    3.41000e-01  2.74580e-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

diff --git a/share/top/oplsaa.ff/ions.itp b/share/top/oplsaa.ff/ions.itp
index 9e82720ab33f69583f3c3f7f5a42953cca8df8f3..83c21cac87fe8a1aead6269664fffeaa413a2497 100644 (file)
--- a/share/top/oplsaa.ff/ions.itp
+++ b/share/top/oplsaa.ff/ions.itp
@@ -10,14 +10,6 @@ CU          1
 ; 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
-ZN          1
-
-[ atoms ]
-; id    at type res nr  residu name at name  cg nr  charge   mass
-1       Zn2+    1       ZN          ZN       1      2        65.37000
-
 [ moleculetype ]
 ; molname   nrexcl
 MG          1