[gmx-users] How to cap a single residue in gromacs (Alessandra Villa) (Justin Lemkul)
Justin Lemkul
jalemkul at vt.edu
Fri Feb 21 01:53:03 CET 2020
On 2/20/20 4:49 PM, Sadaf Rani wrote:
> Dear Justin, thank you for your reply. I have also tried adding ACE and
> NME as below but it didn't work.
Please provide your full command and entire screen output, including any
applicable errors. Saying something "didn't work" is impossible to diagnose.
Note also that your coordinates are completely nonfunctional because all
of the ACE and NME atoms are at (0,0,0) so all the atoms overlap. It
will be hopeless to try to proceed with such coordinates. You need to
actually construct the atoms, not just enter dummy values.
-Justin
> 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
>
> Could you please suggest how should I do that?
>
> Thanks
>
> Sadaf
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com
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