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cp2k/tests/Fist/sample_pot/arginine.pot
Teodoro Laino 5d1f34491b New connectivity generation routines (linear scaling).. faster.. more robust than older one. 
Introduced the possibility to modify by input the generated connectivity.
Bug fix in the neighbour_lists of fist for non-periodic case.
cleaned the particle_types routine.
created a new section in the subsys section called GENERATE that contains all
possible parameters influencing the generation of the connectivity.

Added few more regtests for the new connectivity generator.


svn-origin-rev: 5403
2006-09-19 16:37:41 +00:00

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*>>>>>>> AMBER FF Converted into CHARMM FF style <<<<<<<
*>>>>>>> Generated on :: 20060918 150956.552 +0200 by :: teo <<<<<<<
*>>>>>>> pcihpc07 <<<<<<<
*>>>>>>> Leap Title :: NGLY <<<<<<<
*>>>>>>> Send all comments related to the FFs conversion to <<<<<<<
*>>>>>>> teodoro.laino@gmail.com <<<<<<<
BONDS
!
!V(bond) = Kb(b - b0)**2
!
!Kb: kcal/mole/A**2
!b0: A
!
!atom type Kb b0
!
CT1 HP 340.000000000 1.090000000
N3 H11 434.000000000 1.010000000
N22 H4 434.000000000 1.010000000
N21 H3 434.000000000 1.010000000
CT5 H13 340.000000000 1.090000000
CT4 HC2 340.000000000 1.090000000
CT3 HC1 340.000000000 1.090000000
CT2 H12 340.000000000 1.090000000
N1 H2 434.000000000 1.010000000
CT6 H14 340.000000000 1.090000000
N23 H5 434.000000000 1.010000000
C1 O1 570.000000000 1.229000000
C1 N1 490.000000000 1.335000000
CT1 C1 317.000000000 1.522000000
N3 CT1 367.000000000 1.471000000
C2 O21 570.000000000 1.229000000
C2 N23 490.000000000 1.335000000
CA N22 481.000000000 1.340000000
N21 CA 481.000000000 1.340000000
CT5 N21 337.000000000 1.463000000
CT4 CT5 310.000000000 1.526000000
CT3 CT4 310.000000000 1.526000000
CT2 CT3 310.000000000 1.526000000
CT2 C2 317.000000000 1.522000000
N1 CT2 337.000000000 1.449000000
C3 O22 656.000000000 1.250000000
CT6 C3 317.000000000 1.522000000
N23 CT6 337.000000000 1.449000000
ANGLES
!
!V(angle) = Ktheta(Theta - Theta0)**2
!
!V(Urey-Bradley) = Kub(S - S0)**2
!
!Ktheta: kcal/mole/rad**2
!Theta0: degrees
!Kub: kcal/mole/A**2 (Urey-Bradley)
!S0: A
!
!atom types Ktheta Theta0 Kub S0
!
C1 N1 H2 30.000000000 120.000051429
HP CT1 C1 50.000000000 109.500046929
HP CT1 HP 35.000000000 109.500046929
H11 N3 CT1 50.000000000 109.500046929
H11 N3 H11 35.000000000 109.500046929
N3 CT1 HP 50.000000000 109.500046929
C2 N23 H5 30.000000000 120.000051429
H4 N22 H4 35.000000000 120.000051429
CA N22 H4 35.000000000 120.000051429
H3 N21 CA 35.000000000 120.000051429
H13 CT5 N21 50.000000000 109.500046929
H13 CT5 H13 35.000000000 109.500046929
CT5 N21 H3 35.000000000 118.400050743
HC2 CT4 CT5 50.000000000 109.500046929
HC2 CT4 HC2 35.000000000 109.500046929
CT4 CT5 H13 50.000000000 109.500046929
HC1 CT3 CT4 50.000000000 109.500046929
HC1 CT3 HC1 35.000000000 109.500046929
CT3 CT4 HC2 50.000000000 109.500046929
H12 CT2 CT3 50.000000000 109.500046929
H12 CT2 C2 50.000000000 109.500046929
CT2 CT3 HC1 50.000000000 109.500046929
H2 N1 CT2 30.000000000 118.040050474
N1 CT2 H12 50.000000000 109.500046929
H14 CT6 C3 50.000000000 109.500046929
H14 CT6 H14 35.000000000 109.500046929
H5 N23 CT6 30.000000000 118.040050474
N23 CT6 H14 50.000000000 109.500046929
O1 C1 N1 80.000000000 122.900052672
C1 N1 CT2 50.000000000 121.900052243
CT1 C1 O1 80.000000000 120.400051601
CT1 C1 N1 70.000000000 116.600049972
N3 CT1 C1 80.000000000 111.200047658
O21 C2 N23 80.000000000 122.900052672
C2 N23 CT6 50.000000000 121.900052243
N22 CA N22 70.000000000 120.000051429
N21 CA N22 70.000000000 120.000051429
CT5 N21 CA 50.000000000 123.200052801
CT4 CT5 N21 80.000000000 111.200047658
CT3 CT2 C2 63.000000000 111.100047615
CT3 CT4 CT5 40.000000000 109.500046929
CT2 CT3 CT4 40.000000000 109.500046929
CT2 C2 O21 80.000000000 120.400051601
CT2 C2 N23 70.000000000 116.600049972
N1 CT2 CT3 80.000000000 109.700047015
N1 CT2 C2 63.000000000 110.100047186
O22 C3 O22 80.000000000 126.000054001
CT6 C3 O22 70.000000000 117.000050143
N23 CT6 C3 63.000000000 110.100047186
DIHEDRALS
!
!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
!
!Kchi: kcal/mole
!n: multiplicity
!delta: degrees
!
!atom types Kchi n delta
!
O1 C1 N1 H2 2.000000000 1 0.000000000
O1 C1 N1 H2 2.500000000 2 180.000077144
C1 N1 CT2 H12 0.000000000 2 0.000000000
HP CT1 C1 O1 0.000000000 2 0.000000000
HP CT1 C1 N1 0.000000000 2 0.000000000
CT1 C1 N1 H2 2.500000000 2 180.000077144
H11 N3 CT1 HP 0.155555556 3 0.000000000
H11 N3 CT1 C1 0.155555556 3 0.000000000
O21 C2 N23 H5 2.000000000 1 0.000000000
O21 C2 N23 H5 2.500000000 2 180.000077144
C2 N23 CT6 H14 0.000000000 2 0.000000000
H4 N22 CA N22 2.400000000 2 180.000077144
H3 N21 CA N22 2.400000000 2 180.000077144
N21 CA N22 H4 2.400000000 2 180.000077144
H13 CT5 N21 H3 0.000000000 3 0.000000000
H13 CT5 N21 CA 0.000000000 3 0.000000000
HC2 CT4 CT5 H13 0.155555556 3 0.000000000
HC2 CT4 CT5 N21 0.155555556 3 0.000000000
CT4 CT5 N21 H3 0.000000000 3 0.000000000
HC1 CT3 CT2 C2 0.155555556 3 0.000000000
HC1 CT3 CT4 HC2 0.155555556 3 0.000000000
HC1 CT3 CT4 CT5 0.155555556 3 0.000000000
CT3 CT4 CT5 H13 0.155555556 3 0.000000000
H12 CT2 CT3 HC1 0.155555556 3 0.000000000
H12 CT2 CT3 CT4 0.155555556 3 0.000000000
H12 CT2 C2 O21 0.000000000 2 0.000000000
H12 CT2 C2 N23 0.000000000 2 0.000000000
CT2 CT3 CT4 HC2 0.155555556 3 0.000000000
CT2 C2 N23 H5 2.500000000 2 180.000077144
H2 N1 CT2 H12 0.000000000 2 0.000000000
H2 N1 CT2 CT3 0.000000000 2 0.000000000
H2 N1 CT2 C2 0.000000000 2 0.000000000
N1 CT2 CT3 HC1 0.155555556 3 0.000000000
H14 CT6 C3 O22 0.000000000 2 0.000000000
H5 N23 CT6 H14 0.000000000 2 0.000000000
H5 N23 CT6 C3 0.000000000 2 0.000000000
O1 C1 N1 CT2 2.500000000 2 180.000077144
C1 N1 CT2 CT3 0.530000000 1 0.000000000
C1 N1 CT2 CT3 0.150000000 3 180.000077144
C1 N1 CT2 CT3 0.500000000 4 180.000077144
C1 N1 CT2 C2 0.200000000 2 180.000077144
CT1 C1 N1 CT2 2.500000000 2 180.000077144
N3 CT1 C1 O1 0.000000000 2 0.000000000
N3 CT1 C1 N1 0.000000000 2 0.000000000
O21 C2 N23 CT6 2.500000000 2 180.000077144
C2 N23 CT6 C3 0.200000000 2 180.000077144
CT5 N21 CA N22 2.400000000 2 180.000077144
CT4 CT3 CT2 C2 0.155555556 3 0.000000000
CT4 CT5 N21 CA 0.000000000 3 0.000000000
CT3 CT2 C2 O21 0.000000000 2 0.000000000
CT3 CT2 C2 N23 0.070000000 2 0.000000000
CT3 CT2 C2 N23 0.100000000 4 0.000000000
CT3 CT4 CT5 N21 0.155555556 3 0.000000000
CT2 CT3 CT4 CT5 0.155555556 3 0.000000000
CT2 C2 N23 CT6 2.500000000 2 180.000077144
N1 CT2 CT3 CT4 0.155555556 3 0.000000000
N1 CT2 C2 O21 0.000000000 2 0.000000000
N1 CT2 C2 N23 0.750000000 1 180.000077144
N1 CT2 C2 N23 1.350000000 2 180.000077144
N1 CT2 C2 N23 0.400000000 4 180.000077144
N23 CT6 C3 O22 0.000000000 2 0.000000000
CA H4 N22 H4 1.000000000 2 180.000077144
CT5 CA N21 H3 1.000000000 2 180.000077144
C1 CT2 N1 H2 1.000000000 2 180.000077144
C2 CT6 N23 H5 1.000000000 2 180.000077144
CT1 N1 C1 O1 10.500000000 2 180.000077144
CT2 N23 C2 O21 10.500000000 2 180.000077144
N21 N22 CA N22 10.500000000 2 180.000077144
CT6 O22 C3 O22 10.500000000 2 180.000077144
IMPROPER
!
!V(improper) = Kpsi(psi - psi0)**2
!
!Kpsi: kcal/mole/rad**2
!psi0: degrees
!note that the second column of numbers (0) is ignored
!
!atom types Kpsi psi0
!
NONBONDED
!
!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
!
!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
!
!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
!
N3 0.000000000 0.170000000 1.824000000
H11 0.000000000 0.015700000 0.600000000
CT1 0.000000000 0.109400000 1.908000000
HP 0.000000000 0.015700000 1.099999999
C1 0.000000000 0.086000000 1.908000000
O1 0.000000000 0.210000000 1.661200000
N1 0.000000000 0.170000000 1.824000000
H2 0.000000000 0.015700000 0.600000000
CT2 0.000000000 0.109400000 1.908000000
H12 0.000000000 0.015700000 1.386999999
CT3 0.000000000 0.109400000 1.908000000
HC1 0.000000000 0.015700000 1.487000000
CT4 0.000000000 0.109400000 1.908000000
HC2 0.000000000 0.015700000 1.487000000
CT5 0.000000000 0.109400000 1.908000000
H13 0.000000000 0.015700000 1.386999999
N21 0.000000000 0.170000000 1.824000000
H3 0.000000000 0.015700000 0.600000000
CA 0.000000000 0.086000000 1.908000000
N22 0.000000000 0.170000000 1.824000000
H4 0.000000000 0.015700000 0.600000000
C2 0.000000000 0.086000000 1.908000000
O21 0.000000000 0.210000000 1.661200000
N23 0.000000000 0.170000000 1.824000000
H5 0.000000000 0.015700000 0.600000000
CT6 0.000000000 0.109400000 1.908000000
H14 0.000000000 0.015700000 1.386999999
C3 0.000000000 0.086000000 1.908000000
O22 0.000000000 0.210000000 1.661200000
END
!
! This Section can be cutted & pasted into the Fist input file..
!
CHARGES
N3 0.294300000
H11 0.164200000
CT1 -0.010000000
HP 0.089500000
C1 0.616300001
O1 -0.572200002
N1 -0.347900000
H2 0.274700000
CT2 -0.263700000
H12 0.156000000
CT3 -0.000700000
HC1 0.032700000
CT4 0.039000000
HC2 0.028500000
CT5 0.048600000
H13 0.068700000
N21 -0.529500000
H3 0.345600000
CA 0.807600001
N22 -0.862699999
H4 0.447800000
C2 0.734099998
O21 -0.589399999
N23 -0.382100000
H5 0.268100000
CT6 -0.249300000
H14 0.105600000
C3 0.723099998
O22 -0.785500003
END CHARGES
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