[gmx-users] Multiple dihedral types in .rtp file

[Anton Feenstra]

Chris O'Brien wrote:
> Hello all,
> 
> I am trying to model a polymer using GROMACS.  Because it uses a 
> non-standard residue, I am adding one (actually 5) to the ffgmx.rtp 
> file.  I would like to use both a Ryckaert-Bellemans and a periodic 
> function to best describe the dihedral rotation barriers.  What format 
> do I need to use to get this to work?  Can I just use two [ bondedtypes 
> ] lines at the beginning of the file that will only differ in the 
> dihedrals column?  Can I define bondedtypes specifically for each 
> residue?  However it is done, I want to make sure it won't interfere 
> with the built-in residues in the file because others will be using 
> GROMACS here as well.

You can include explicit parameters directly in the .rtp file, which will
only affect those residues. Using bondedtypes directives (in the ffgmxbon.itp
file), you cannot define two functions on the same set of atoms. In stead
of really explicit parameters in the .rtp, you can also use the method that
is used in the Gromos forcefield (ffG43*), where in the ff*bon.itp a
#define is used to attach parameters to a label, and this label is inserted
in the .rtp file. This way, you will keep the separation between topology
info (rtp) and parameters (ff*bon.itp).


-- 
Groetjes,

Anton
  ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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