[gmx-users] VAL group

[Mark Abraham]

Owen, Michael wrote:
> 
> Hello gmx users,
> 
> when I convert a pdb file of a peptide that contains a valyl residue 
> into a .gro file a separate "group" is made for the atoms in the valyl 
> residue.

In what sense...? please include a relevant file excerpt, and the 
commands that created it.

>  This has happened when OPLSAA/l and the GROMOS96 53a6 force 
> fields were used.  The molecule appears as one in the topology file,  
> and the atomic description of the valyl residue in the pdb file matches 
> that of the ffoplsa.rtp file.

Have these forcefields really being modified for a radical, or are you 
really describing a valine residue?

Mark