[gmx-users] Index file
Giannis Gl
igaldadas at gmail.com
Tue May 26 20:32:55 CEST 2015
Dear all,
I am very amateur in GROMACS, so please forgive my silly question.
I want to group the following atoms
ATOM 2285b C1 LIG X 6 32.880 59.958 110.850 0.00
0.00
ATOM 2285c CL1 LIG X 6 31.972 61.400 110.520 0.00
0.00
ATOM 2285d N1 LIG X 6 32.318 58.744 110.532 0.00
0.00
ATOM 2285e C2 LIG X 6 33.272 57.852 110.816 0.00
0.00
ATOM 2285f N2 LIG X 6 34.376 58.450 111.368 0.00
0.00
ATOM 22860 C3 LIG X 6 34.138 59.800 111.370 0.00
0.00
ATOM 22861 C4 LIG X 6 35.550 57.768 111.896 0.00
0.00
ATOM 22862 H1 LIG X 6 35.550 57.880 112.984 0.00
0.00
ATOM 22863 H2 LIG X 6 35.460 56.692 111.730 0.00
0.00
ATOM 22864 C5 LIG X 6 34.992 60.962 111.784 0.00
0.00
ATOM 22865 H3 LIG X 6 35.626 61.290 110.956 0.00
0.00
ATOM 22866 H4 LIG X 6 34.380 61.822 112.070 0.00
0.00
ATOM 22867 O1 LIG X 6 35.840 60.652 112.888 0.00
0.00
ATOM 22868 H5 LIG X 6 36.496 60.016 112.550 0.00
0.00
ATOM 22869 C6 LIG X 6 33.084 56.380 110.604 0.00
0.00
ATOM 2286a H6 LIG X 6 33.950 55.966 110.086 0.00
0.00
ATOM 2286b H7 LIG X 6 33.040 55.868 111.568 0.00
0.00
ATOM 2286c C7 LIG X 6 31.828 56.028 109.792 0.00
0.00
ATOM 2286d H8 LIG X 6 30.938 56.388 110.312 0.00
0.00
ATOM 2286e H9 LIG X 6 31.860 56.538 108.828 0.00
0.00
ATOM 2286f C8 LIG X 6 31.688 54.518 109.558 0.00 0.00
...
but the command,
a 2285b-2286f
or the command,
a 2285b 2285c 2285d ... 2286f
doesn't recognize atoms' numbers followed by a character
"Found 0 atoms with names 2285B 2285C"
Is there any other way that I could select these atoms?
I know I could try a dynamic selection (g_select), but unfortunately, my
pdb file contains 10 ligands and all of them have the same resname. Thus,
there is no feature besides the atom
that I could use to destinguish them. Even the coordinates are useless;
there are ligands with
almost the same x-coordinate but different y.
Thanking you in advance!
I hope I made clear my problem and didn't confuse you.
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