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
