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
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