[gmx-users] Re: amb2gmx.pl to convert GLYCAM topology

[Yun Shi]

Hi all,

I am not a CS person, but I did find something in acpype.py as

.............
                if phase in [0, 180]:
                    properDihedralsGmx45.append([item[0].atoms, phaseRaw,
kPhi, period])
                    if not self.gmx45:
                        if kPhi > 0: V[period] = 2 * kPhi * cal
                        if period == 1:
                            C[0] += 0.5 * V[period]
                            if phase == 0:
                                C[1] -= 0.5 * V[period]
                            else:
                                C[1] += 0.5 * V[period]
                        elif period == 2:
......................

kPhi here seems to be the dihedral force constant, and it seems if kPhi < 0,
no value will be assigned to C[0], C[1], C[2] ...

I wonder if the negative dihedral force constants problem could be solved by
changing 'kPhi > 0' to 'kPhi != 0' for acpype?

Thanks,

Yun
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