[gmx-users] virtual sites in gromacs
Tsjerk Wassenaar
tsjerkw at gmail.com
Wed Sep 18 07:23:21 CEST 2013
Hi Neha,
Yes. The MN* particles are the virtual sites.
Cheers,
Tsjerk
On Wed, Sep 18, 2013 at 7:13 AM, Neha Gandhi <n.gandhiau at gmail.com> wrote:
> 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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--
Tsjerk A. Wassenaar, Ph.D.
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