Hi, I wonder if there is a general way to generate the correct params file of new beta and gamma NCAA ? I am trying to parameterize a customized gamma amino acid residue for GenKIC application. I used the molfile_to_params_polymer.py to generate .params file from the .mol file attached below:
4CG.pdb
OpenBabel04262311383D
29 28 0 0 1 0 0 0 0 0999 V2000
-5.3100 -4.8280 2.6840 N 0 0 0 0 0 0 0 0 0 0 0 0
-6.1510 -4.0380 3.5820 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.6510 -4.3310 2.0960 H 0 0 0 0 0 0 0 0 0 0 0 0
-5.9440 -2.9740 3.4550 H 0 0 0 0 0 0 0 0 0 0 0 0
-5.9530 -4.3120 4.6210 H 0 0 0 0 0 0 0 0 0 0 0 0
-7.2060 -4.2180 3.3650 H 0 0 0 0 0 0 0 0 0 0 0 0
-5.3490 -6.1570 2.5880 C 0 0 0 0 0 0 0 0 0 0 0 0
-6.1220 -6.8300 3.2710 O 0 0 0 0 0 0 0 0 0 0 0 0
-3.9150 -10.3980 0.3570 N 0 0 0 0 0 0 0 0 0 0 0 0
-4.3800 -6.7990 1.5900 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.4810 -8.3380 1.5130 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.5680 -8.9740 0.4470 C 0 0 1 0 0 0 0 0 0 0 0 0
-2.0580 -8.7540 0.7560 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.4320 -9.5120 1.5060 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.4470 -7.7040 0.2120 N 0 0 0 0 0 0 0 0 0 0 0 0
-3.4240 -11.0310 0.9730 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.3710 -6.5110 1.8830 H 0 0 0 0 0 0 0 0 0 0 0 0
-4.5840 -6.3770 0.6050 H 0 0 0 0 0 0 0 0 0 0 0 0
-4.2370 -8.7640 2.4890 H 0 0 0 0 0 0 0 0 0 0 0 0
-5.5140 -8.6000 1.2780 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.7760 -8.4940 -0.5110 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.9510 -7.0790 -0.3990 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.4720 -7.5460 0.4120 H 0 0 0 0 0 0 0 0 0 0 0 0
-4.9810 -12.4060 -0.4250 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.7960 -10.9110 -0.4860 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.4360 -10.2300 -1.2810 O 0 0 0 0 0 0 0 0 0 0 0 0
-5.3130 -12.6860 0.5740 H 0 0 0 0 0 0 0 0 0 0 0 0
-4.0320 -12.8940 -0.6430 H 0 0 0 0 0 0 0 0 0 0 0 0
-5.7260 -12.7140 -1.1570 H 0 0 0 0 0 0 0 0 0 0 0 0
1 3 1 0 0 0 0
1 2 1 0 0 0 0
1 7 1 0 0 0 0
2 4 1 0 0 0 0
2 5 1 0 0 0 0
2 6 1 0 0 0 0
7 8 2 0 0 0 0
7 10 1 0 0 0 0
9 16 1 0 0 0 0
9 12 1 0 0 0 0
9 25 1 0 0 0 0
10 17 1 0 0 0 0
10 18 1 0 0 0 0
10 11 1 0 0 0 0
11 19 1 0 0 0 0
11 20 1 0 0 0 0
11 12 1 0 0 0 0
12 21 1 6 0 0 0
12 13 1 0 0 0 0
13 14 2 0 0 0 0
13 15 1 0 0 0 0
15 22 1 0 0 0 0
15 23 1 0 0 0 0
24 25 1 0 0 0 0
24 27 1 0 0 0 0
24 28 1 0 0 0 0
24 29 1 0 0 0 0
25 26 2 0 0 0 0
M ROOT 7
M POLY_N_BB 7
M POLY_CA_BB 10
M POLY_C_BB 7
M POLY_O_BB 8
M POLY_IGNORE 2 4 5 6 3 24 27 28 29 26
M POLY_UPPER 1
M POLY_LOWER 25
M POLY_CHG 0
M POLY_PROPERTIES PROTEIN GAMMA_AA POLAR
M END
But molfile_to_params_polymer.py gives me polymer type .params file with duplicated HA and connections as below:
NAME 4CG
IO_STRING 4CG X
TYPE POLYMER
AA UNK
ATOM N Nbb C 0.61
ATOM CA CAbb CT2 -0.19
ATOM O OCbb O -0.56
ATOM CB CH2 CT2 -0.19
ATOM CG CH1 CT1 -0.10
ATOM ND1 Ntrp NH1 -0.62
ATOM CD2 COO C 0.61
ATOM OE1 ONH2 O -0.56
ATOM NE2 NH2O NH2 -0.48
ATOM HA Hapo HB 0.08
ATOM HA Hapo HB 0.08
ATOM 1HB Hapo HA 0.08
ATOM 2HB Hapo HA 0.08
ATOM 1HG Hapo HA 0.08
ATOM 1HD1 Hpol H 0.42
ATOM 1HE2 Hpol H 0.42
ATOM 2HE2 Hpol H 0.42
BOND N O
BOND N CA
BOND ND1 1HD1
BOND ND1 CG
BOND CA HA
BOND CA HA
BOND CA CB
BOND CB 1HB
BOND CB 2HB
BOND CB CG
BOND CG 1HG
BOND CG CD2
BOND CD2 OE1
BOND CD2 NE2
BOND NE2 1HE2
BOND NE2 2HE2
LOWER_CONNECT N
UPPER_CONNECT C
CHI 1 N CA CB CG
CHI 2 CA CB CG ND1
CHI 3 CB CG CD2 OE1
NBR_ATOM CB
NBR_RADIUS 6.964028
FIRST_SIDECHAIN_ATOM CB
PROPERTIES PROTEIN GAMMA_AA POLAR
ICOOR_INTERNAL N 0.000000 180.000000 1.532034 CA N N
ICOOR_INTERNAL CA 0.000000 180.000000 1.532034 N CA N
ICOOR_INTERNAL N 0.000000 180.000000 1.532034 CA N N
ICOOR_INTERNAL UPPER 0.000000 63.500431 1.333033 N CA N
ICOOR_INTERNAL O 0.000000 58.046918 1.231644 N CA N
ICOOR_INTERNAL CB -179.427009 65.873986 1.544232 CA N UPPER
ICOOR_INTERNAL CG 176.413274 65.978102 1.540916 CB CA N
ICOOR_INTERNAL ND1 -171.852472 72.383720 1.468429 CG CB CA
ICOOR_INTERNAL LOWER 0.000000 139.796380 5.688216 N CA N
ICOOR_INTERNAL 1HD1 178.457578 62.918331 1.010557 ND1 CG LOWER
ICOOR_INTERNAL CD2 -123.991199 67.726508 1.556914 CG CB ND1
ICOOR_INTERNAL OE1 85.228323 58.347236 1.236503 CD2 CG CB
ICOOR_INTERNAL NE2 -178.670448 61.604839 1.331074 CD2 CG OE1
ICOOR_INTERNAL 1HE2 -1.133616 59.545604 1.008941 NE2 CD2 CG
ICOOR_INTERNAL 2HE2 -179.466397 60.877973 1.007764 NE2 CD2 1HE2
ICOOR_INTERNAL 1HG -118.204384 71.774443 1.091526 CG CB CD2
ICOOR_INTERNAL 1HB 122.146199 70.764445 1.092515 CB CA CG
ICOOR_INTERNAL 2HB 117.406752 71.825478 1.091310 CB CA 1HB
ICOOR_INTERNAL HA -121.892522 72.553396 1.089437 CA N CB
ICOOR_INTERNAL HA -116.575863 72.072047 1.090837 CA N HA
Best Regards