Tutorial 7: Supercell of a Molecule
In this tutorial, we will show you how to use pdbtop to prepare a molecule from crystal information file.
A Human-Friendly Structure
Assume we want to study a molecule extracted from a crystal file, like below:
152
26.82330000 0.00000000 0.00000000 -0.61173682 7.61747610 0.00000000 -2.88460658 -3.00446059 10.11298264
3 F 3.20571333 1.57108292 8.64215044
4 N -0.01000558 1.36877398 5.42065982
5 F -0.18209647 5.88197647 0.79821772
6 C -1.19930474 0.78322729 5.61472796
7 C 4.97105834 0.05673124 4.57814724
8 C 5.63578345 -0.09158089 3.36458932
9 H 5.22756058 -0.58646481 2.66375963
10 C 0.05684111 0.47005996 3.16637486
11 H 0.52680596 0.36225562 2.34722327
12 C 0.58837131 1.20165159 4.21913636
13 H 1.43408579 1.61426635 4.08665628
14 N -1.78584940 0.90741634 6.83769095
15 H 4.25956295 0.50412048 6.91829142
16 C -1.34573501 1.57535447 7.98419979
17 C -2.33210951 1.91487621 8.91054900
18 C -2.04149970 2.57198395 10.07556460
19 C 2.13466065 5.91632188 0.28518611
20 H 2.33762127 6.36779272 1.09624732
21 C 0.24883758 2.56937763 9.49204550
22 H 1.15021747 2.79249767 9.69228256
23 C -0.03236361 1.91615442 8.30882654
24 H 0.67332038 1.69578534 7.71216056
25 C 3.64481584 -0.56113934 4.77332781
26 O 2.97973169 -0.44724045 5.80272831
27 O 2.60913597 6.35161846 3.72754427
28 H 1.89161804 5.96240297 3.92484856
29 F 0.12124328 3.04193258 1.47083220
30 N 3.33696219 3.24424152 4.69232281
31 F 3.50905308 -1.26896097 9.31476492
32 C 4.52626135 3.82978822 4.49825468
33 C -1.64410173 4.55628426 5.53483540
34 C -2.30882685 4.70459639 6.74839332
35 H -1.90060397 5.19948032 7.44922301
36 C 3.27011550 4.14295554 6.94660777
37 H 2.80015065 4.25075988 7.76575937
38 C 2.73858530 3.41136392 5.89384628
39 H 1.89287082 2.99874915 6.02632635
40 N 5.11280601 3.70559917 3.27529169
41 H -0.93260634 4.10889503 3.19469122
42 C 4.67269162 3.03766103 2.12878285
43 C 5.65906612 2.69813930 1.20243364
44 C 5.36845631 2.04103156 0.03741804
45 C 1.19229596 -1.30330638 9.82779653
46 H 0.98933534 -1.75477721 9.01673532
47 C 3.07811903 2.04363788 0.62093713
48 H 2.17673913 1.82051783 0.42070008
49 C 3.35932022 2.69686109 1.80415610
50 H 2.65363623 2.91723016 2.40082208
51 C -0.31785924 5.17415484 5.33965483
52 O 0.34722492 5.06025595 4.31025433
53 O 0.71782064 -1.73860296 6.38543837
54 H 1.43533857 -1.34938747 6.18813408
The structure is shown below:
This strucutre is very ugly and is not human-friendly. However, if we know its lattice cell information, we can use a single command to convert it into a good structure:
$ pdbtop ligand -i 4501688.xyz --pbc "6.82330000 0.00000000 0.00000000 -0.61173682 7.61747610 0.00000000 -2.88460658 -3.00446059 10.11298264" -o adjust
There are two sets of output:
adjust.*: The output based on the original structure;adjust-sc.*: The output based on the converted structure.
The structure of adjust-sc.pdb is shown below, which looks much better than the original one:
Build Supercells
Assume we want to study this molecule in crystal environment, we can build a supercell, like 5x5x5, so we can use the option --super-cells:
$ pdbtop ligand -i 4501688.xyz --pbc "6.82330000 0.00000000 0.00000000 -0.61173682 7.61747610 0.00000000 -2.88460658 -3.00446059 10.11298264" --super-cells "2 2 2" -o supercell
Here, “–super-cells 2 2 2” means we include the 2 images in the direction of +X,-X,+Y,-Y,+Z,-Z. The output structure supercell-sc.pdb is shown below:
