From owner-chemistry@ccl.net Fri Aug 29 13:57:00 2014
From: "Andrew DeYoung andrewdaviddeyoung##gmail.com" <owner-chemistry() server.ccl.net>
To: CCL
Subject: CCL: What does PHE(OL) mean?
Message-Id: <-50455-140829132626-1428-P0GL1OO8xxROfCAbCpILZA() server.ccl.net>
X-Original-From: Andrew DeYoung <andrewdaviddeyoung%%gmail.com>
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Date: Fri, 29 Aug 2014 13:26:19 -0400
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Sent to CCL by: Andrew DeYoung [andrewdaviddeyoung=gmail.com]
Hi,

This might be more of a biochemistry question rather than a
computational chemistry 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