[gmx-users] Re: modeling a chromophore residue

[David van der Spoel]

On Wed, 10 Oct 2001, Luke Czapla wrote:

>  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!

OK, I've attached the pdb file with atoms and residues renamed, for you to
check.
What needs doing here is a midified THR and GLY residue in rtp and hdb
file (THX and GLX or something like that). The THX will not have O, while
the GLX will not have H. The pdb file residues for THX should be renamed.
Then you have to make an entry in the specbond file which looks like
GLY	N	1	THX	C	1	0.138	GLX	THX
where 0.138 is the bond length

The only remaing item is the charge, which is probably not very high,
typically -0.1 for N and 0.1 for C. This will make the residues have
non-integer charge.

The final final thing is the improper dihedrals for keeping the ring flat.
You may have to add these manually. The question is how flat it should
be....

Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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HEADER    Giant Rising Ordinary Mutants for A Clerical Setup
MODEL
HETATM    1  N   THR     1      -3.167  -0.414  -1.850  1.00 20.000
HETATM    2  CA  THR     1      -2.233  -1.449  -1.382  1.00 20.000
HETATM    3  CB  THR     1      -1.313  -1.892  -2.530  1.00 20.000
HETATM    4  CG  THR     1      -2.089  -2.505  -3.664  1.00 20.000
HETATM    5  OG  THR     1      -0.565  -0.798  -2.999  1.00 20.000
HETATM    6  C   THR     1      -1.514  -0.821  -0.215  1.00 20.000
HETATM    7  N   TYR     2      -0.269  -0.195  -0.244  1.00 20.000
HETATM    8  C   TYR     2      -1.201  -0.052   1.910  1.00 20.000
HETATM    9  O   TYR     2      -1.222   0.035   3.106  1.00 20.000
HETATM   10  CA  TYR     2      -0.047   0.318   1.052  1.00 20.000
HETATM   11  CB  TYR     2       1.085   0.895   1.500  1.00 20.000
HETATM   12  CG  TYR     2       2.193   1.443   0.664  1.00 20.000
HETATM   13  CD  TYR     2       2.297   1.176  -0.718  1.00 20.000
HETATM   14  CD  TYR     2       3.243   2.183   1.345  1.00 20.000
HETATM   15  CE  TYR     2       3.463   1.619  -1.427  1.00 20.000
HETATM   16  CE  TYR     2       4.370   2.636   0.625  1.00 20.000
HETATM   17  CZ  TYR     2       4.474   2.373  -0.739  1.00 20.000
HETATM   18  OH  TYR     2       5.650   2.877  -1.489  1.00 20.000
HETATM   19  N   GLY     3      -1.970  -0.803   1.049  1.00 20.000
HETATM   20  CA  GLY     3      -3.325  -1.206   1.382  1.00 20.000
HETATM   21  C   GLY     3      -3.499  -2.601   1.900  1.00 20.000
HETATM   22  O   GLY     3      -4.359  -2.811   2.733  1.00 20.000
TER
ENDMDL