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Andreas Krämer's avatar
added broken tests for issue #2353  
Andreas Krämer committed
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* STREAM FILE FOR ENVIRONMENT
*

set nat ?NATC
set app
!We're exploiting what is arguably a bug in the parser. On the left hand side,
!the quotes have priority, so NAT is correctly substituted. On the right hand
!side, the ? has priority and NATC" (sic) is not a valid substitution...
if "@NAT" ne "?NATC" if @nat ne 0 set app append


READ RTF CARD @{app}
* Constructed Based on Stream File from CGenff
*
36 1

MASS  -1  CCX2     12.01100  C
MASS  -1  HCX2      1.00800  H
MASS  -1  OCX1     15.99940  O
MASS  -1  HOX1      1.00800  H
MASS  -1  CCX3     12.01100  C
MASS  -1  HCX3      1.00800  H
MASS  -1   HT       1.00800  H 
MASS  -1   OT      15.99940  O 
MASS  -1  CLA      35.45000  CL
MASS  -1  POT      39.09830  K 

DEFA FIRS NONE LAST NONE
AUTO ANGLES DIHE DRUDE

RESI OCOH     0.000 ! PARAM_PENALTY=0.0000 ; CHARGE_PENALTY=0.0000
GROUP            ! CHARGE   CH_PENALTY
ATOM C1     CCX2    0.050 !    0.000
ATOM H11    HCX2    0.090 !    0.000
ATOM H12    HCX2    0.090 !    0.000
ATOM O1     OCX1   -0.649 !    0.000
ATOM HO1    HOX1    0.420 !    0.000
ATOM C2     CCX2   -0.181 !    0.000
ATOM H21    HCX2    0.090 !    0.000
ATOM H22    HCX2    0.090 !    0.000
ATOM C3     CCX2   -0.180 !    0.000
ATOM H31    HCX2    0.090 !    0.000
ATOM H32    HCX2    0.090 !    0.000
ATOM C4     CCX2   -0.180 !    0.000
ATOM H41    HCX2    0.090 !    0.000
ATOM H42    HCX2    0.090 !    0.000
ATOM C5     CCX2   -0.180 !    0.000
ATOM H51    HCX2    0.090 !    0.000
ATOM H52    HCX2    0.090 !    0.000
ATOM C6     CCX2   -0.180 !    0.000
ATOM H61    HCX2    0.090 !    0.000
ATOM H62    HCX2    0.090 !    0.000
ATOM C7     CCX2   -0.180 !    0.000
ATOM H71    HCX2    0.090 !    0.000
ATOM H72    HCX2    0.090 !    0.000
ATOM C8     CCX3   -0.270 !    0.000
ATOM H81    HCX3    0.090 !    0.000
ATOM H82    HCX3    0.090 !    0.000
ATOM H83    HCX3    0.090 !    0.000

BOND H12  C1  
BOND H31  C3  
BOND H51  C5  
BOND H71  C7  
BOND H42  C4  
BOND H22  C2  
BOND H62  C6  
BOND H82  C8  
BOND C1   H11 
BOND C1   C2  
BOND C1   O1  
BOND C3   C2  
BOND C3   C4  
BOND C3   H32 
BOND C5   C4  
BOND C5   C6  
BOND C5   H52 
BOND C7   C6  
BOND C7   C8  
BOND C7   H72 
BOND H83  C8  
BOND C2   H21 
BOND C4   H41 
BOND C6   H61 
BOND C8   H81 
BOND HO1  O1  

RESI TIP3         0.000 
GROUP
ATOM OH2  OT     -0.834
ATOM H1   HT      0.417
ATOM H2   HT      0.417
BOND OH2 H1 OH2 H2 H1 H2    ! the last bond is needed for shake
ANGLE H1 OH2 H2             ! required
DONOR H1 OH2
DONOR H2 OH2
ACCEPTOR OH2
PATCHING FIRS NONE LAST NONE

RESI POT       1.00 ! Potassium Ion
GROUP
ATOM POT   POT 1.00
PATCHING FIRST NONE LAST NONE

RESI CLA      -1.00 ! Chloride Ion
GROUP
ATOM CLA  CLA -1.00
PATCHING FIRST NONE LAST NONE

END

READ PARA CARD FLEX @{APP}
* PARAMETERS FOR ENVIR
*


ATOMS
MASS  -1  CCX2     12.01100 ! CGENFF_PRM
MASS  -1  HCX2      1.00800 ! CGENFF_PRM
MASS  -1  OCX1     15.99940 ! CGENFF_PRM
MASS  -1  HOX1      1.00800 ! CGENFF_PRM
MASS  -1  CCX3     12.01100 ! CGENFF_PRM
MASS  -1  HCX3      1.00800 ! CGENFF_PRM
MASS  -1  HT        1.00800 ! CGENFF_PRM 
MASS  -1  OT       15.99940 ! CGENFF_PRM
MASS  -1  CLA      35.45000 ! CGENFF_PRM
MASS  -1  POT      39.09830 ! CGENFF_PRM


BONDS
CCX2  CCX2    222.500    1.5300 ! CGENFF_PRM
CCX2  CCX3    222.500    1.5280 ! CGENFF_PRM
CCX2  OCX1    428.000    1.4200 ! CGENFF_PRM
CCX2  HCX2    309.000    1.1110 ! CGENFF_PRM
CCX3  HCX3    322.000    1.1110 ! CGENFF_PRM
OCX1  HOX1    545.000    0.9600 ! CGENFF_PRM
HT    HT        0.0      1.5139 ! CGENFF_PRM
HT    OT      450.000    0.9572 ! CGENFF_PRM

ANGLES
CCX2   CCX2   CCX2     58.350   113.6000    11.160   2.5610 ! CGENFF_PRM
CCX2   CCX2   CCX3     58.000   115.0000     8.000   2.5610 ! CGENFF_PRM
CCX2   CCX2   OCX1     75.700   110.1000 ! CGENFF_PRM
CCX2   CCX2   HCX2     26.500   110.1000    22.530   2.1790 ! CGENFF_PRM
CCX3   CCX2   HCX2     34.600   110.1000    22.530   2.1790 ! CGENFF_PRM
OCX1   CCX2   HCX2     45.900   108.8900 ! CGENFF_PRM
HCX2   CCX2   HCX2     35.500   109.0000     5.400   1.8020 ! CGENFF_PRM
CCX2   CCX3   HCX3     34.600   110.1000    22.530   2.1790 ! CGENFF_PRM
HCX3   CCX3   HCX3     35.500   108.4000     5.400   1.8020 ! CGENFF_PRM
CCX2   OCX1   HOX1     50.000   106.0000 ! CGENFF_PRM
HT     OT     HT       55.000   104.5200 ! CGENFF_PRM   

DIHEDRALS
CCX2  CCX2  CCX2  CCX2      0.0645  2    0.00 ! CGENFF_PRM
CCX2  CCX2  CCX2  CCX2      0.1497  3  180.00 ! CGENFF_PRM
CCX2  CCX2  CCX2  CCX2      0.0946  4    0.00 ! CGENFF_PRM
CCX2  CCX2  CCX2  CCX2      0.1125  5    0.00 ! CGENFF_PRM
CCX2  CCX2  CCX2  CCX3      0.1505  2    0.00 ! CGENFF_PRM
CCX2  CCX2  CCX2  CCX3      0.0813  3  180.00 ! CGENFF_PRM
CCX2  CCX2  CCX2  CCX3      0.1082  4    0.00 ! CGENFF_PRM
CCX2  CCX2  CCX2  CCX3      0.2039  5    0.00 ! CGENFF_PRM
CCX2  CCX2  CCX2  OCX1      0.1950  3    0.00 ! CGENFF_PRM
CCX2  CCX2  CCX2  HCX2      0.1950  3    0.00 ! CGENFF_PRM
CCX3  CCX2  CCX2  HCX2      0.1800  3    0.00 ! CGENFF_PRM
OCX1  CCX2  CCX2  HCX2      0.1950  3    0.00 ! CGENFF_PRM
HCX2  CCX2  CCX2  HCX2      0.2200  3    0.00 ! CGENFF_PRM
CCX2  CCX2  CCX3  HCX3      0.1600  3    0.00 ! CGENFF_PRM
HCX2  CCX2  CCX3  HCX3      0.1600  3    0.00 ! CGENFF_PRM
CCX2  CCX2  OCX1  HOX1      1.1300  1    0.00 ! CGENFF_PRM
CCX2  CCX2  OCX1  HOX1      0.1400  2    0.00 ! CGENFF_PRM
CCX2  CCX2  OCX1  HOX1      0.2400  3    0.00 ! CGENFF_PRM
HCX2  CCX2  OCX1  HOX1      0.1800  3    0.00 ! CGENFF_PRM

IMPROPERS

NONBONDED nbxmod  5 atom cdiel fshift vatom vdistance vfswitch -
cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
CCX2    0.0      -0.0560   2.0100  0.0  -0.0100  1.9000 ! CGENFF_PRM
HCX2    0.0      -0.0350   1.3400 ! CGENFF_PRM
OCX1    0.0      -0.1921   1.7650 ! CGENFF_PRM
HOX1    0.0      -0.0460   0.2245 ! CGENFF_PRM
CCX3    0.0      -0.0780   2.0500  0.0  -0.0100  1.9000 ! CGENFF_PRM
HCX3    0.0      -0.0240   1.3400 ! CGENFF_PRM
HT       0.0     -0.0460   0.2245 ! CGENFF_PRM
OT       0.0     -0.1521   1.7682 ! CGENFF_PRM
POT      0.0     -0.0870   1.76375 ! CGENFF_PRM 
CLA      0.0     -0.1500   2.27    ! CGENFF_PRM


NBFIX
POT    CLA      -0.114236   4.081 ! CGENFF_PRM 

HBOND CUTHB 0.5

END