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 <alanwil...@gmail.com
<mailto:alanwil...@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-requ...@gromacs.org
<mailto:gmx-users-requ...@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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