[gmx-users] converting ILDN parameters to RB

[David van der Spoel]

On 2011-03-31 17.19, Alan Wilter Sousa da Silva wrote:
> I know it's supported.
>
> I was just investigating the possibility since I build acpype to create
> topologies for gromacs, but also it converts from amber to gromacs (like
> amb2gmx.pl <http://amb2gmx.pl>), and so I was wondering about RB with 6
> coefficients since multiple proper dihedrals is only supported for gmx
> 4.5 and above.
Unfortunately RB only goes to 5 and it would be a pain to support more 
since the tpr format would have to be updated. The current solution with 
the type 9 dihedrals is a royal pain in the neck too. I've actually 
written a script that converts the present rtp files to contain *all* 
bonded interactions explicitly (with parameters), and it replaces the 9 
type dihedrals with multiple 1 type dihedrals (lots of them with all 
zeros, LOL).
>
> But I don't want to fuss about it. If to forget about GMX 4.0.x and
> below is the way, so it will be.
>
> Thanks,
>
> Alan
>
> On 31 March 2011 16:08, David van der Spoel <spoel at xray.bmc.uu.se
> <mailto:spoel at xray.bmc.uu.se>> wrote:
>
>     On 2011-03-31 15.27, Alan Wilter Sousa da Silva wrote:
>
>         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:
>
>     ILDN is already supported in the latest gromacs releases, by simply
>     using multiple proper dihedrals. Why would you want to change it?
>
>
>
>         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
>
>
>
>     --
>     David van der Spoel, Ph.D., Professor of Biology
>     Dept. of Cell & Molec. Biol., Uppsala University.
>     Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>     spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
>     http://folding.bmc.uu.se
>     --
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>
>
>
> --
> Alan Wilter SOUSA da SILVA, DSc
> Bioinformatician, UniProt - PANDA, EMBL-EBI
> CB10 1SD, Hinxton, Cambridge, UK
> +44 1223 49 4588
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se