[gmx-users] virtual sites in gromacs

[Neha Gandhi]

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