[gmx-users] Force field problems

[Mark Abraham]

Michael McGovern wrote:
> Hello everyone,
> 
>    I'm working with a peptide-like molecule that is covalently bonded to a linker.  For the peptide-like part I am using a modified version of the ffG53a6 force field files.  The linker section contains an alkyl section, an oligo-ethylene glycol section (...-O-CH2-CH2-O-CH2-CH2...) and two sulfur atoms.
> 
>   I am having difficulty finding parameters for this linker section that are compatible with the peptide section.  I can parametrize it with ffgmx, but it is not compatible with the peptide section when they are combined in the same molecule.  Does anyone have any ideas that might be helpful?  Thanks a lot.

AMBER's GAFF is intended to provide a reasonable approach to these 
situations, and such a force field can be expressed in GROMACS.

Mark