[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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