[gmx-users] What does PHE(OL) mean?
adeyoung at andrew.cmu.edu
Tue Aug 26 18:57:52 CEST 2014
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
Thanks so much for your time!
Carnegie Mellon University
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