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Fluorescent residue



I'm attempting to make a model of a protein containing a fluorescent residue attached to a specific Lysine. The structure of the Lysyl-fluorophore is: (view it in a fixed font).
                           Cl
                          /
NH2                     N-C
|                      /   \
CH-CH2-CH2-CH2-CH2-NH-C    N  H H
|                      \   /  | |
C=02H                   N-C   C-C    CH2-CH3
                          \ /   \  /
                           C    C-N
                            \   /  \
                             C-C    CH2-CH3
                             | |
                             H H

Both rings are aromatic, but I couldn't represent that above. I've modified all of the necessary files to account for the radius and mass of the Chlorine, and the name (TAK or t)of the new residue. I'm attaching a text file of one of my attempts to define this residue in the top_heav.lib file. Now I'm starting to modify the parameter file (par.lib), and have figured out at least part of how to do that, but modifying that file does not seem to give me a better looking residue. This residue should be flat from the 1st side chain N to the last N(CH2)2, including both rings. Mine generally come out slightly bent! The attached file assumes no changes to the parameter file. Can anyone give me help beyond what is in the manual? Thanks for your attention. John
--

John T. Penniston, Ph.D.
Dept. of Biochemistry and Molecular Biology
Guggenheim 16, Mayo Clinic
200 First St. SW
Rochester, MN 55905 USA


RESI TAK	  0.00000
ATOM N    NH1    -0.17091
ATOM CA   CT1     0.11455
ATOM CB   CT2    -0.06545
ATOM CG   CT2    -0.06545
ATOM CD   CT2    -0.06545
ATOM CE   CT2     0.066
ATOM NZ1  NH1    -0.293
ATOM CH1  CPH2    0.488
ATOM NQ1  NN3A   -0.387
ATOM NQ2  NN3A   -0.406
ATOM CI1  CN5      0.390
ATOM CI2  CN2      0.544
ATOM NK1  NN3A   -0.29091
ATOM CLK  CL	 -0.318
ATOM CK1  CA     -0.055
ATOM CL1  CA     -0.002
ATOM CL2  CA     -0.001
ATOM CM1  CA     -0.115
ATOM CM2  CA     -0.114
ATOM CN1  CA      0.198
ATOM NX1  NH1    -0.228
ATOM CO1  CT2     0.074
ATOM CP1  CT3    -0.166
ATOM CO2  CT2     0.074
ATOM CP2  CT3    -0.166 
ATOM C    C       0.83455
ATOM O    O      -0.18545
BOND CB CA  CG CB  CD CG  CE CD  NZ1 CE  CH1  NZ1
BOND NQ1 CH1  NQ2 CH1  CI1 NQ1  CI2 NQ2  NK1 CI1
BOND NK1 CI2  CLK CI2
BOND CK1 CI1  CL1 CK1  CL2 CK1  CM1 CL1  CM2 CL2
BOND CN1 CM1  CN1 CM2  CN1 NX1  NX1 CO1  NX1 CO2
BOND CO1 CP1  CO2 CP2
BOND N CA  O C  C CA  C +N
IMPR C CA +N O  CA N C CB  CE NZ1 CH1 NQ1
IMPR NZ1 CH1 NQ1 CI1  CH1 NQ1 CI1 NK1  NQ1 CI1 NK1 CI2
IMPR CI1 NK1 CI2 NQ2  NK1 CI2 NQ2 CH1  CI2 NQ2 CH1 NZ1
IMPR CE NZ1 CH1 NQ1  
IMPR CI1 NK1 CI2 CLK  CH1 NQ2 CI2 CLK  !CH1 NQ1 CI1 CK1
IMPR CI2 NK1 CI1 CK1  CK1 CI1 NK1 CI2
IMPR CL2 CL1 CK1 CI1  CL1 CK1 CI1 NK1  CL2 CK1 CI1 NQ1
IMPR CI1 CK1 CL1 CM1  !CI1 CK1 CL2 CM2
IMPR CK1 CL1 CM1 CN1  CL1 CM1 CN1 CM2
IMPR CM1 CN1 CM2 CL2  CN1 CM2 CL2 CK1
IMPR CL1 CM1 CN1 NX1  CL2 CM2 CN1 NX1
IMPR CM1 CM2 CI1 CLK  CM1 CI1 NZ1 NQ2
IMPR NK1 NQ1 NQ2 NZ1  NK1 CI1 CI2 CH1  CHI NQ1 NQ2 NK1
IMPR CI1 CLK CH1 NQ1
IC -C    N     CA    C         1.3496  122.4500  180.0000  109.8600    1.5227
IC N     CA    C     +N        1.4544  109.8600  180.0000  117.1200    1.3511
IC +N    CA    *C    O         1.3511  117.1200  180.0000  121.4000    1.2271
IC CA    C     +N    +CA       1.5227  117.1200  180.0000  124.6700    1.4565
IC N     C     *CA   CB        1.4544  109.8600  123.6400  112.2600    1.5552
IC N     CA    CB    CG        1.4544  110.7000  180.0000  115.9500    1.5475
IC CA    CB    CG    CD        1.5552  115.9500  180.0000  114.0100    1.5384
IC CB    CG    CD    CE        1.5552  115.9500  180.0000  114.0100    1.5384
IC CG    CD    CE    NZ1       1.5475  114.0100  180.0000  107.09      1.45
IC CD    CE    NZ1   CH1       1.5384  107.0900  180.0000  120.00      1.35
IC CE    NZ1   CH1   NQ1       1.45    120.00    180.0000  120.00      1.26
IC NZ1   NQ2   *CH1  NQ1       1.35    120.0000  180.0000  120.00      1.26!
IC NQ1   NZ1   *CH1  NQ2       1.26    120.0000  180.0000  120.00      1.26!
IC NZ1   CH1   NQ1   CI1       1.35    120.0000 -180.0000  120.00      1.26
IC NZ1   CH1   NQ2   CI2       1.35    120.0000 -180.0000  120.00      1.26
IC CH1   NQ1   CI1   NK1       1.26    120.0000   -0.1900  120.00      1.26
IC NK1   NQ2   *CI2  CLK       1.26    120.0000 -180.0000  120.00      1.72
IC NK1   NQ1   *CI1  CK1       1.26    120.0000 -180.0000  120.00      1.4
IC NQ1   CI1   CK1   CL1       1.2600  120.0000  180.0000  120.00      1.4
IC NQ1   CI1   CK1   CL1       1.2600  120.0000  180.0000  120.00      1.4
IC NK1   CI1   *CK1  CL2       1.27    120.0000 -180.0000  120.00      1.4
IC CI1   CK1   CL1   CM1       1.4     120.0000 -180.0000  120.00      1.4
IC CI1   CK1   CL2   CM2       1.4     120.0000 -180.0000  120.00      1.4
IC CK1   CL2   CM2   CN1       1.4     120.0000  0.000     120.00      1.4
IC CK1   CL1   CM1   CN1       1.4     120.0000  180.000   120.00      1.4
IC CL1   CK1   CI1   NK1       1.4     120.0000  180.000   120.00      1.26
IC CN1   NX1   CO1   CP1       1.35    120.0     120.      109.        1.53
IC CM1   CN1   NX1   CO1       1.4     120.0    -180.       120.        1.46
IC CN1   NX1   CO2   CP2       1.35    120.0     120.      109.        1.53
IC CM2   CN1   NX1   CO2       1.4     120.0     180.       120.        1.46
IC CM2   CM1   *CN1  NX1       1.4     120.5500 -178.9800  120.4100    1.35
PATC FIRS NTER LAST CTER