[gmx-users] How to cap a single residue in gromacs

Sadaf Rani sadafrani6 at gmail.com
Tue Feb 18 16:30:03 CET 2020


Dear Gromacs users
I am trying to make a system with 1 single amino acid(PHE) and 1 Ligand
when I run pdb2gmx it gives me error:-
Fatal error:
In the chosen force field there is no residue type for 'PHE' as a standalone
(starting & ending) residue

I added ACE and NME terminals as below in the gro file:-

1ACE     HC    1   0.000   0.000   0.000  0.0000  0.0000  0.0000
    1ACE     CT    2   0.000   0.000   0.000  0.0000  0.0000  0.0000
    1ACE     HC    3   0.000   0.000   0.000  0.0000  0.0000  0.0000
    1ACE     HC    4   0.000   0.000   0.000  0.0000  0.0000  0.0000
    1ACE      C    5   0.000   0.000   0.000  0.0000  0.0000  0.0000
    1ACE      O    6   0.000   0.000   0.000  0.0000  0.0000  0.0000
    2PHE      N    7   5.066   4.671   6.042  0.2692 -0.2632  0.1330
    2PHE      H    8   5.027   4.600   5.982 -1.5227  1.0889 -0.3963
    2PHE     CA    9   5.013   4.811   6.023  0.0535  0.3709  0.0960
    2PHE     HA   10   5.058   4.868   6.105 -1.0081  1.0531  0.2242
    2PHE     CB   11   5.052   4.871   5.883 -0.0860  0.7332  0.2870
    2PHE    HB1   12   4.990   4.822   5.809  1.1212 -0.4628  0.0312
    2PHE    HB2   13   5.153   4.841   5.853  0.2157  2.3973 -0.5141
    2PHE     CG   14   5.062   5.017   5.867  0.0161  0.4565  0.5724
    2PHE    CD1   15   4.951   5.101   5.874 -0.1757 -0.2234 -0.3056
    2PHE    HD1   16   4.855   5.054   5.884 -0.9265  1.6156  2.3658
    2PHE    CE1   17   4.958   5.242   5.856 -0.3304  0.7195  0.1599
    2PHE    HE1   18   4.866   5.298   5.857  0.2928  1.7852 -0.4831
    2PHE     CZ   19   5.085   5.297   5.832 -0.3945 -1.0394 -0.7463
    2PHE     HZ   20   5.101   5.404   5.842 -0.5983 -1.2279  3.1660
    2PHE    CE2   21   5.200   5.216   5.830 -0.1669 -0.6131  1.1550
    2PHE    HE2   22   5.293   5.264   5.804 -1.0122  1.2508  1.4080
    2PHE    CD2   23   5.186   5.075   5.852  0.3885  0.2183 -0.6920
    2PHE    HD2   24   5.276   5.015   5.847 -0.0823 -0.3875 -3.1559
    2PHE      C   25   4.859   4.799   6.042  0.1650 -0.6772  0.7098
    2PHE      O   26   4.794   4.721   5.968  0.0339  0.0386 -0.1578
    3NME      N   27   0.000   0.000   0.000  0.0000  0.0000  0.0000
    3NME      H   28   0.000   0.000   0.000  0.0000  0.0000  0.0000
    3NME     CT   29   0.000   0.000   0.000  0.0000  0.0000  0.0000
    3NME     H1   30   0.000   0.000   0.000  0.0000  0.0000  0.0000
    3NME     H1   31   0.000   0.000   0.000  0.0000  0.0000  0.0000
    3NME     H1   32   0.000   0.000   0.000  0.0000  0.0000  0.0000
    4G6P      P   33   5.063   5.809   5.979  0.5468  0.1315 -0.0198
    4G6P    O1P   34   5.208   5.823   5.982  0.3151 -0.5087  0.1960
    4G6P    O2P   35   5.020   5.704   6.075  0.0937 -0.0791 -0.0538
    4G6P    O3P   36   5.028   5.939   6.039 -0.2953  0.3030 -0.2016
    4G6P     C1   37   4.985   5.671   5.430  0.5407  0.1917  0.2635
    4G6P     O1   38   5.118   5.662   5.388 -0.4011  0.4548 -0.8044
    4G6P     C2   39   4.889   5.558   5.383  0.3352  0.1447  0.3610
    4G6P     O2   40   4.876   5.546   5.239 -0.2019 -0.6192 -1.0434
    4G6P     C3   41   4.753   5.566   5.458  0.0668  0.4155 -0.3386
    4G6P     O3   42   4.674   5.438   5.425 -0.8214  0.3092 -0.1367
    4G6P     C4   43   4.783   5.561   5.611  0.3702 -0.3821 -0.5929
    4G6P     O4   44   4.661   5.608   5.676 -0.1025  0.6063 -0.0795
    4G6P     C5   45   4.890   5.667   5.654 -0.3851  0.4555 -0.1137
    4G6P     O5   46   5.006   5.658   5.573 -0.0288  0.1296 -0.6207
    4G6P     C6   47   4.935   5.670   5.809 -0.1636  0.0426  0.3771
    4G6P     O6   48   5.001   5.791   5.841  0.2972 -0.6933 -0.1489
    4G6P     H1   49   4.939   5.768   5.412  2.0772  1.3511  2.0534
    4G6P     H2   50   4.932   5.464   5.418  0.0848 -0.0506  0.1425
    4G6P     H3   51   4.706   5.660   5.427  0.9723  0.2387 -2.4228
    4G6P     H4   52   4.804   5.459   5.646 -0.3467 -0.2084  0.3693
    4G6P     H5   53   4.845   5.766   5.640 -0.6619  0.2119 -1.0742
    4G6P    H61   54   5.002   5.587   5.833  2.3826  1.5930 -0.8342
    4G6P    H62   55   4.851   5.665   5.878  1.0230  1.5442  2.0329
    4G6P    HO1   56   5.160   5.619   5.465  0. 23 -0.1270 -1.6233
    4G6P    HO2   57   4.816   5.469   5.232 -0.0502 -0.7762 -0.6581
    4G6P    HO3   58   4.671   5.441   5.328  0.3044  0.1862 -0.1954
    4G6P    HO4   59   4.649   5.553   5.755 -1.5501  2.1018  0.8000

However, it still claims the same error.
How should I add this in force field file? How can I use -ter command that
it can add N and C termini itself to the residue?
I would really thankful for your suggestions.
Thanks.

Sadaf


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