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

Carla Jamous carlajamous at gmail.com
Thu Oct 22 13:46:20 CEST 2009

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.


On Tue, Oct 20, 2009 at 5:16 PM, Alan <alanwilter at gmail.com> wrote:

> Dear Carla,
> Let me suggest you the wikis at 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> 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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