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

[Johnny Lu]

may be the paper about the force field talk about that?



On Tue, Aug 26, 2014 at 12:24 PM, Andrew DeYoung <adeyoung at andrew.cmu.edu>
wrote:

> 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
>
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