AMBER Archive (2009)

Subject: [AMBER] Source of new CYX residue parameters in ff03ua

From: Chris Moth (chris.moth_at_Vanderbilt.Edu)
Date: Tue Apr 07 2009 - 14:48:46 CDT

I noticed that Amber10 may have introduced a CYX residue in the
Yang et al united item forcefield CYX was not present in Amber9 and
earlier (diff command below).

I am curious as to how the parameters were added to the force field.
Might there be a reference?

Apologies in advance if CYX introduction is documented in an online
changelog which I failed to locate.

Thanks

Chris
-----------------------------------------------------------------

diff ..../amber10/..../dat/leap/lib/uni_amino03.lib
..../amber9/..../dat/leap/lib/uni_amino03.lib | head -20

8d7
< "CYX"
567,645d565
< !entry.CYX.unit.atoms table str name str type int typex int resx
int flags int seq int elmnt dbl chg
< "N" "N" 0 1 131072 1 7 -0.435921
< "H" "H" 0 1 131072 2 1 0.290077
< "CA" "CT" 0 1 131072 3 6 -0.016965
< "HA" "H1" 0 1 131072 4 1 0.118305
< "CB" "C2" 0 1 131072 5 6 -0.193674
< "SG" "S" 0 1 131072 6 16 -0.200793
< "C" "C" 0 1 131072 7 6 0.624788
< "O" "O" 0 1 131072 8 8 -0.573167
< !entry.CYX.unit.atomspertinfo table str pname str ptype int ptypex
int pelmnt dbl pchg
< "N" "N" 0 -1 0.0
< "H" "H" 0 -1 0.0
< "CA" "CT" 0 -1 0.0
< "HA" "H1" 0 -1 0.0
< "CB" "C2" 0 -1 0.0
< "SG" "S" 0 -1 0.0
< "C" "C" 0 -1 0.0

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