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bug fix for onfo for 5 and 6 membered rings.. introducing 2 specific regtests..

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resetting loop.inp.


svn-origin-rev: 5188
This commit is contained in:
Teodoro Laino 2006-05-24 20:41:46 +00:00
parent f100c4362d
commit bdfc9a5712
13 changed files with 619 additions and 18 deletions
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123
tests/Fist/sample_pot/cyhex.pot Normal file
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@ -0,0 +1,123 @@
*>>>>>>> AMBER FF Converted into CHARMM FF style <<<<<<<
*>>>>>>> Generated on :: 20060524 214647.502 +0200 by :: teo <<<<<<<
*>>>>>>> pcihpc07 <<<<<<<
*>>>>>>> Leap Title :: MOL <<<<<<<
*>>>>>>> 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
!
c31 hc1 337.300000000 1.092000000
c32 hc2 337.300000000 1.092000000
c33 hc3 337.300000000 1.092000000
o c 648.000000000 1.214000000
c c31 328.300000000 1.508000000
c31 c32 303.100000000 1.535000000
c32 c33 303.100000000 1.535000000
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
!
c c31 hc1 47.200000000 109.680046777
c31 c32 hc2 46.400000000 110.050047451
hc1 c31 hc1 39.400000000 108.350046723
hc1 c31 c32 46.400000000 110.050047451
c32 c33 hc3 46.400000000 110.050047451
hc2 c32 hc2 39.400000000 108.350046723
hc2 c32 c33 46.400000000 110.050047451
hc3 c33 hc3 39.400000000 108.350046723
o c c31 68.000000000 123.110052590
c c31 c32 63.800000000 110.530047428
c31 c c31 62.800000000 116.050050023
c31 c32 c33 63.200000000 110.630047471
c32 c33 c32 63.200000000 110.630047471
DIHEDRALS
!
!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
!
!Kchi: kcal/mole
!n: multiplicity
!delta: degrees
!
!atom types Kchi n delta
!
o c c31 hc1 0.800000000 1 0.000000000
o c c31 hc1 0.080000000 3 180.000077144
o c c31 hc1 0.000000000 2 180.000077144
c c31 c32 hc2 0.155555556 3 0.000000000
c31 c c31 hc1 0.000000000 2 180.000077144
c31 c32 c33 hc3 0.160000000 3 0.000000000
hc1 c31 c32 hc2 0.150000000 3 0.000000000
hc1 c31 c32 c33 0.160000000 3 0.000000000
c32 c33 c32 hc2 0.160000000 3 0.000000000
hc2 c32 c33 hc3 0.150000000 3 0.000000000
o c c31 c32 0.000000000 2 180.000077144
c c31 c32 c33 0.155555556 3 0.000000000
c31 c c31 c32 0.000000000 2 180.000077144
c31 c32 c33 c32 0.200000000 1 180.000077144
c31 c32 c33 c32 0.250000000 2 180.000077144
c31 c32 c33 c32 0.180000000 3 0.000000000
o c c31 c31 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
!
o 0.000000000 0.210000000 1.661200000
c 0.000000000 0.086000000 1.908000000
c31 0.000000000 0.109400000 1.908000000
hc1 0.000000000 0.015700000 1.487000000
c32 0.000000000 0.109400000 1.908000000
hc2 0.000000000 0.015700000 1.487000000
c33 0.000000000 0.109400000 1.908000000
hc3 0.000000000 0.015700000 1.487000000
END
!
! This Section can be cutted & pasted into the Fist input file..
!
CHARGES
o -0.541370000
c 0.458570000
c31 0.005880000
hc1 0.010000000
c32 0.012980000
hc2 0.004150000
c33 -0.005170000
hc3 -0.003170000
END CHARGES

108
tests/Fist/sample_pot/pentadiene.pot Normal file
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*>>>>>>> AMBER FF Converted into CHARMM FF style <<<<<<<
*>>>>>>> Generated on :: 20060524 153444.174 +0200 by :: teo <<<<<<<
*>>>>>>> pcihpc07 <<<<<<<
*>>>>>>> Leap Title :: MOL <<<<<<<
*>>>>>>> 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
!
c2 ha1 344.300000000 1.087000000
c3 hc 337.300000000 1.092000000
ce ha2 341.500000000 1.089000000
c2 c3 328.300000000 1.508000000
c2 ce 560.500000000 1.339000000
ce ce 390.500000000 1.451000000
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
!
c2 c3 hc 47.000000000 110.490047525
c2 ce ha2 49.600000000 121.100051901
ha1 c2 c3 45.700000000 117.300050272
ha1 c2 ce 49.600000000 121.190052111
hc c3 hc 39.400000000 108.350046723
ce ce ha2 47.500000000 115.900049672
c2 c3 c2 64.600000000 109.710046847
c2 ce ce 65.700000000 123.080052520
c3 c2 ce 65.700000000 117.400050315
DIHEDRALS
!
!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
!
!Kchi: kcal/mole
!n: multiplicity
!delta: degrees
!
!atom types Kchi n delta
!
c2 c3 c2 ha1 0.000000000 2 0.000000000
c2 ce ce ha2 1.000000000 2 180.000077144
ha1 c2 c3 hc 0.000000000 2 0.000000000
ha1 c2 ce ce 6.650000000 2 180.000077144
ha1 c2 ce ha2 6.650000000 2 180.000077144
c3 c2 ce ha2 6.650000000 2 180.000077144
ce c2 c3 hc 0.000000000 2 0.000000000
ha2 ce ce ha2 1.000000000 2 180.000077144
c2 c3 c2 ce 0.000000000 2 0.000000000
c2 ce ce c2 1.000000000 2 180.000077144
c3 c2 ce ce 6.650000000 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
!
c2 0.000000000 0.086000000 1.908000000
ha1 0.000000000 0.015000000 1.459000000
c3 0.000000000 0.109400000 1.908000000
hc 0.000000000 0.015700000 1.487000000
ce 0.000000000 0.086000000 1.908000000
ha2 0.000000000 0.015000000 1.459000000
END
!
! This Section can be cutted & pasted into the Fist input file..
!
CHARGES
c2 -0.238180000
ha1 0.132210000
c3 0.088690000
hc 0.051510000
ce -0.129140000
ha2 0.139260000
END CHARGES