[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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