[gmx-users] Re: converting proper dihedrals into ryckaert-bellemans

[Mark Abraham]

Carla Jamous wrote:
> Dear Alan,
> if I completely understood how acpypi works, it seems that it generates 
> the topology parameters from the pdb file of the molecule.
> But the problem is that I have the topology parameters (my angles, bond 
> distances and dihedrals) and want to implement them in Gromacs, so 
> actually I want to set specific parameters' values in gromacs.
> 
> Carla

This is why the manual is so long :-) Chapter 4 talks about the 
functional forms that can be used, and chapter 5 discusses how these are 
implemented in the force field files. You'll need to have started by 
reading these. Converting a sum of proper dihedrals into R-B form just 
requires knowledge of basic trigonometry identities.

Mark

> On Tue, Oct 20, 2009 at 5:16 PM, Alan <alanwilter at gmail.com 
> <mailto:alanwilter at gmail.com>> wrote:
> 
>     Dear Carla,
> 
>     Let me suggest you the wikis at acpypi.googlecode.com
>     <http://acpypi.googlecode.com>.
> 
>     And then let me ask why amber94 and not amber99sb? And why not trying
>     acpypi in the link above as I guess it can do pretty much what you
>     want with much less pain?
> 
>     Cheers,
>     Alan
> 
>     On Tue, Oct 20, 2009 at 15:55,  <gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>> wrote:
>      >
>      > Hi everyone,
>      > I'm using the amber94 force field in gromacs. I need to add
>     topology of a
>      > new molecule for my MD simulation.
>      > I saw this line "propers treated as RBs in GROMACS to use combine
>     multiple
>      > AMBER torsions per quartet" in my ffamber94bon.itp file.
>      > So it seems that I have to convert my proper dihedrals parameters
>     into RB
>      > parameters, in order to run my simulation.
>      > Does anyone have an idea of how can I do this, to have the right
>     parameters
>      > for my molecule?
>      >
>      > Thanks a lot
>      >
>      > Carla
> 
>     --
>     Alan Wilter Sousa da Silva, D.Sc.
>     PDBe group, PiMS project http://www.pims-lims.org/
>     EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10
>     1SD, UK
>     +44 (0)1223 492 583 (office)
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