[gmx-users] modeling a chromophore residue

[Luke Czapla]

Greetings David and list,

  Here is the PDB file for the definition of the chromophore found in many
Green Fluorescent Proteins.  This is a residue formed by oxidation of the
sequence Ser-Tyr-Gly.  We have gotten good advice on how to treat the Tyr
in the middle (which is unmodified except for an oxidation to a double
bond of the CA-CB bond) but we want to form the heterocycle (an
imidizol-1-one) that results from bonding between the Ser carbonyl C and
the Gly amino N. If anyone has any advice on how to modify existing .rtp
entries to model this it would be very helpful.   Otherwise some advice on
creating a brand new entry would be excellent.  Thanks!

HETATM    1  N1  CRO   964      -3.167  -0.414  -1.850  1.00 20.00
HETATM    2  CA1 CRO   964      -2.233  -1.449  -1.382  1.00 20.00
HETATM    3  CB1 CRO   964      -1.313  -1.892  -2.530  1.00 20.00
HETATM    4  CG1 CRO   964      -2.089  -2.505  -3.664  1.00 20.00
HETATM    5  OG1 CRO   964      -0.565  -0.798  -2.999  1.00 20.00
HETATM    6  C1  CRO   964      -1.514  -0.821  -0.215  1.00 20.00
HETATM    7  N2  CRO   964      -0.269  -0.195  -0.244  1.00 20.00
HETATM    8  N3  CRO   964      -1.970  -0.803   1.049  1.00 20.00
HETATM    9  C2  CRO   964      -1.201  -0.052   1.910  1.00 20.00
HETATM   10  O2  CRO   964      -1.222   0.035   3.106  1.00 20.00
HETATM   11  CA2 CRO   964      -0.047   0.318   1.052  1.00 20.00
HETATM   12  CA3 CRO   964      -3.325  -1.206   1.382  1.00 20.00
HETATM   13  C3  CRO   964      -3.499  -2.601   1.900  1.00 20.00
HETATM   14  O3  CRO   964      -4.359  -2.811   2.733  1.00 20.00
HETATM   15  CB2 CRO   964       1.085   0.895   1.500  1.00 20.00
HETATM   16  CG2 CRO   964       2.193   1.443   0.664  1.00 20.00
HETATM   17  CD1 CRO   964       2.297   1.176  -0.718  1.00 20.00
HETATM   18  CD2 CRO   964       3.243   2.183   1.345  1.00 20.00
HETATM   19  CE1 CRO   964       3.463   1.619  -1.427  1.00 20.00
HETATM   20  CE2 CRO   964       4.370   2.636   0.625  1.00 20.00
HETATM   21  CZ  CRO   964       4.474   2.373  -0.739  1.00 20.00
HETATM   22  OH  CRO   964       5.650   2.877  -1.489  1.00 20.00


Cheers,
Luke Czapla