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