Hi, I have made an all-hydrogen topology file for HYP(4-hydroxyproline). BUT How MODELLER's non-hydrogen topology and other topologies was derived?
I attach my RTF file for HYP as follows:
MASS 30 N 14.00700 N MASS 20 CP1 12.01100 C MASS 6 HB 1.00800 H MASS 23 CC 12.01100 C MASS 44 O 15.99900 O MASS 21 CP2 12.01100 C MASS 3 HA 1.00800 H MASS 13 CT1 12.01100 C MASS 47 OH1 15.99900 O MASS 1 H 1.00800 H MASS 22 CP3 12.01100 C MASS 15 CT3 12.01100 C MASS 11 C 12.01100 C MASS 35 NH2 14.00700 N DECL -N DECL +C
AUTO ANGLES DIHE
RESI HYP 0.00000 GROUP ! HD1 HD2 ATOM N N -0.2900 ! | \ / ATOM CA CP1 0.0200 ! N---CD HG ATOM HA HB 0.0900 ! | \ / GROUP ! | CG ATOM C CC 0.5300 ! | / \ ATOM O O -0.5300 ! HA-CA--CB OG2--HG2 GROUP ! | / \ ATOM CB CP2 -0.1800 ! | HB1 HB2 ATOM HB1 HA 0.0900 ! O=C ATOM HB2 HA 0.0900 ! | GROUP ATOM CG CT1 0.1400 ATOM HG HA 0.0900 ATOM OG2 OH1 -0.6600 ATOM HG2 H 0.4300 GROUP ATOM CD CP3 0.1800 ATOM HD1 HB 0.0000 ATOM HD2 HB 0.0000 BOND N CA N CD CA HA CA CB CA C BOND C O CB HB1 CB HB2 CB CG CG HG BOND CG OG2 CG CD CD HD1 CD HD2 N +C BOND C N OG2 HG2 IMPH N CA CD +C C CA N O DONOR HG2 OG2 ACCEPTOR O C IC CD N CA CB 1.4468 114.9587 -11.2918 101.8808 1.5360 IC CD N CA HA 1.4468 114.9587 -129.2290 110.5162 1.0924 IC CD N CA C 1.4468 114.9587 109.5875 111.6376 1.5380 IC HA CA N +C 1.0924 110.5162 50.0429 122.5076 1.3162 IC CD +C *N CA 1.4468 122.5296 -179.2170 122.5076 1.4550 IC CA N CD CG 1.4550 114.9587 -11.8599 102.4794 1.5305 IC CA N CD HD1 1.4550 114.9587 -131.8901 111.1069 1.0924 IC CA N CD HD2 1.4550 114.9587 106.0401 109.5406 1.0925 IC N CA CB CG 1.4550 101.8808 29.6080 103.6605 1.5362 IC N CA CB HB1 1.4550 101.8808 152.0681 112.9350 1.0925 IC N CA CB HB2 1.4550 101.8808 -86.5729 108.9663 1.0930 IC N CA C O 1.4550 111.6376 149.4002 120.4223 1.2316 IC N CA C N 1.4550 111.6376 -31.0428 120.0469 1.3161 IC N CA *C O 1.3161 120.0469 -179.5571 120.4223 1.2316 IC CA CB CG OG2 1.5360 103.6605 -158.7449 112.5784 1.4300 IC CA CB CG HG 1.5360 103.6605 79.0616 109.5554 1.0926 IC CD CG OG2 HG2 1.5305 112.2089 31.3937 109.5000 1.0300 IC N CD CG CB 1.4468 102.4794 29.9288 103.3139 1.5362 PATC FIRS PROP LAST CTER
Any comment or suggestion for it? Thank you very much! With best regards, Kong Lesheng