[gmx-users] What does PHE(OL) mean?

[Andrew DeYoung]

Hi,

This might be more of a biochemistry question rather than a Gromacs
question, so I apologize in advance...

In the "top" directory (e.g., on my installation, it's
/usr/local/gromacs/share/gromacs/top/) of the Gromacs installation, several
force fields are included.  I'm looking at the file "ffbonded.itp" in the
"oplsaa.ff" directory.  I see, for example, this entry under [ angles ]:

  CA     CA     CA      1   120.000    527.184   ; PHE(OL)

PHE, I'm sure, refers to phenylalanine, where CA is an aromatic carbon.  But
to what does (OL) refer?

I see other (OL) entries in the topology: for example, TYR(OL), TRP(OL), and
ARG(OL)?  Does (OL) somehow refer to the protonation state of the amino
acid?

Thanks so much for your time!

Andrew DeYoung
Carnegie Mellon University