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

[Mark Abraham]

On 13/09/2011 6:21 AM, Yun Shi wrote:
> 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?

Maybe. As I have said on this topic before (check the archives) one 
needs to read the documentation, write out the equations and demonstrate 
their (in)equivalence.

Mark