Removing Zn and Ar non-OPLS atom types

Some parameters were clearly wrong and the source of them was
not documented. They can be added back in but then the source
needs to be documented.

Add source for Fe2+.

Leaving Cu2+, Fe2+ and SI given their source is documented.

Fixes #957

Change-Id: I82a5b7ae4a54ab2aeb5690cea6256146a9819250

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