[gmx-users] converting ILDN parameters to RB

[Alan Wilter Sousa da Silva]

Hi there,

Since ILDN dihedrals has some parameters with up to periodicity 6, I was
wondering if it's possible to convert it in RB with 6 coefficients. If so,
what would be the formula? For example, for converting the usual Amber99SB
to RB I have:

                if phase in [0, 180]:

                    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:

                        if phase == 180:

                            C[0] += V[period]

                            C[2] -= V[period]

                        else:

                            C[2] += V[period]

                    elif period == 3:

                        C[0] += 0.5 * V[period]

                        if phase == 0:

                            C[1] += 1.5 * V[period]

                            C[3] -= 2 * V[period]

                        else:

                            C[1] -= 1.5 * V[period]

                            C[3] += 2 * V[period]

                    elif period == 4:

                        if phase == 180:

                            C[2] += 4 * V[period]

                            C[4] -= 4 * V[period]

                        else:

                            C[0] += V[period]

                            C[2] -= 4 * V[period]

                            C[4] += 4 * V[period]

So, as you can see, I can handle up to 4 periods (C[5] is always 0, but not
with ILDN and I need to add C[6] rules as well).

Any ideas? Many thanks in advance,

Alan
-- 
Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt - PANDA, EMBL-EBI
CB10 1SD, Hinxton, Cambridge, UK
+44 1223 49 4588
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