Dear Users,
I am trying to prepare file using pdb2gmx using Gomos 43a1 ff. I am
using following command.
pdb2gmx -f input.gro -o input1.gro -vsite hydrogens -ignh
Upon visualisation I could see triangle like sites. Does the output seem right?
75
1VAL MN1 1 2.913 3.551 3.288
1VAL MN2 2 2.880 3.575 3.356
1VAL N 3 2.891 3.561 3.320
1VAL H1 4 2.960 3.543 3.250
1VAL H2 5 2.887 3.659 3.339
1VAL H3 6 2.915 3.511 3.403
1VAL CA 7 2.758 3.515 3.271
1VAL CB 8 2.761 3.365 3.234
1VAL CG1 9 2.628 3.322 3.174
1VAL CG2 10 2.878 3.334 3.138
1VAL C 11 2.651 3.542 3.379
1VAL O 12 2.640 3.469 3.476
2GLN N 13 2.578 3.652 3.361
2GLN H 14 2.599 3.711 3.283
2GLN CA 15 2.467 3.691 3.449
2GLN CB 16 2.497 3.826 3.515
2GLN CG 17 2.399 3.863 3.627
2GLN CD 18 2.427 3.999 3.688
2GLN OE1 19 2.428 4.101 3.617
2GLN NE2 20 2.450 4.003 3.818
2GLN HE21 21 2.449 3.918 3.872
2GLN HE22 22 2.469 4.090 3.863
2GLN C 23 2.342 3.700 3.363
2GLN O 24 2.337 3.777 3.269
3ILE N 25 2.242 3.620 3.396
3ILE H 26 2.250 3.564 3.479
3ILE CA 27 2.119 3.610 3.317
3ILE CB 28 2.107 3.470 3.251
3ILE CG1 29 2.228 3.440 3.162
3ILE CG2 30 1.981 3.459 3.168
3ILE CD 31 2.257 3.295 3.151
3ILE C 32 2.000 3.634 3.409
3ILE O 33 1.985 3.563 3.508
4VAL N 34 1.918 3.734 3.379
4VAL H 35 1.936 3.789 3.297
4VAL CA 36 1.802 3.766 3.463
4VAL CB 37 1.817 3.903 3.533
4VAL CG1 38 1.695 3.934 3.619
4VAL CG2 39 1.944 3.903 3.618
4VAL C 40 1.674 3.766 3.381
4VAL O 41 1.664 3.838 3.283
5TYR N 42 1.580 3.682 3.422
5TYR H 43 1.602 3.617 3.494
5TYR CA 44 1.445 3.681 3.366
5TYR CB 45 1.400 3.537 3.337
5TYR CG 46 1.463 3.471 3.217
5TYR CD1 47 1.572 3.386 3.230
5TYR HD1 48 1.610 3.368 3.321
5TYR CD2 49 1.413 3.494 3.089
5TYR HD2 50 1.334 3.555 3.077
5TYR CE1 51 1.629 3.326 3.120
5TYR HE1 52 1.707 3.264 3.131
5TYR CE2 53 1.469 3.434 2.978
5TYR HE2 54 1.431 3.451 2.887
5TYR CZ 55 1.578 3.351 2.993
5TYR OH 56 1.632 3.291 2.882
5TYR HH 57 1.582 3.321 2.800
5TYR C 58 1.352 3.741 3.471
5TYR O 59 1.337 3.685 3.580
6LYS N 60 1.290 3.853 3.439
6LYS H 61 1.306 3.895 3.349
6LYS CA 62 1.197 3.917 3.532
6LYS CB 63 1.271 4.015 3.624
6LYS CG 64 1.323 4.142 3.559
6LYS CD 65 1.428 4.211 3.649
6LYS CE 66 1.468 4.349 3.597
6LYS MNZ1 67 1.590 4.442 3.650
6LYS MNZ2 68 1.594 4.377 3.696
6LYS NZ 69 1.587 4.407 3.670
6LYS HZ1 70 1.608 4.497 3.632
6LYS HZ2 71 1.565 4.416 3.767
6LYS HZ3 72 1.665 4.346 3.659
6LYS C 73 1.080 3.982 3.461
6LYS O1 74 1.065 3.973 3.340
6LYS O2 75 0.988 4.044 3.539
--
Regards,
Dr. Neha S. Gandhi,
Curtin Research Fellow,
School of Biomedical Sciences,
Curtin University,
Perth GPO U1987
Australia
LinkedIn
Research Gate
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