[gmx-users] How to cap a single residue in gromacs
Alessandra Villa
alessandra.villa.biosim at gmail.com
Wed Feb 19 09:23:46 CET 2020
Hi
On Tue, Feb 18, 2020 at 4:30 PM Sadaf Rani <sadafrani6 at gmail.com> wrote:
> 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
>
> NOTE that several atoms in the above gro file have the same (0. 0. 0.)
coordinate/position.
That may cause a crash when you start the simulation
> 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?
>
Yes the first thing I will do is to try is -ter.
Different force fields have different termini definition
(maybe the force field has already ACE and NME)
Best regards
Alessandra
> I would really thankful for your suggestions.
> Thanks.
>
> Sadaf
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