[gmx-users] How to cap a single residue in gromacs
Quyen V. Vu
vuqv.phys at gmail.com
Wed Feb 19 21:13:52 CET 2020
Hi,
Without saying about the physical meaning of your model because I don't
know what you are doing.
About technical point, I used your PHE coordinate and using pymol to cap
with ACE, NME as you said then execute pdb2gmx using amber99sb forcefield
in gromacs, it works well. What is the error that you say?
On Wed, Feb 19, 2020, 09:25 Alessandra Villa <
alessandra.villa.biosim at gmail.com> wrote:
> 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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