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
Hi Sadaf,
You can also try to build your entire system with the prodrg server and consider it as a ligand.
Rajiv Lakkaniga I used AMBER99SB-ILDN protein force field.
Martiniano Bello, Can you please elaborate a bit on how to build it.
Thanks.
Sadaf
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