# [gmx-users] converting ILDN parameters to RB

Alan Wilter Sousa da Silva awilter at ebi.ac.uk
Thu Mar 31 15:27:13 CEST 2011

```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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110331/99d61e0a/attachment.html>
```