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Merge pull request #16 from MobleyLab/latest
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@hannahbaumann
hannahbaumann authored Aug 29, 2022
2 parents 1807bfe + 635805a commit 7f58c39
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1 change: 1 addition & 0 deletions README.md
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# SeparatedTopologies
Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).


## Installation
```bash
# Create conda environment using environment.yml file
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@<TRIPOS>MOLECULE
lig_13
48 51 0 0 0
SMALL
USER_CHARGES

@<TRIPOS>ATOM
1 C1 -33.2652 -45.8563 17.7205 C.1 1 <0> 0.4841
2 C2 -35.3048 -43.5774 15.6028 C.ar 1 <0> -0.1500
3 C3 -34.2044 -44.2521 16.1255 C.ar 1 <0> -0.1500
4 C4 -36.5843 -43.8109 16.1158 C.ar 1 <0> -0.1500
5 C5 -39.2916 -44.9925 16.9342 C.ar 1 <0> -0.1500
6 C6 -40.5536 -45.1949 17.4992 C.ar 1 <0> -0.1500
7 C7 -35.6691 -45.4106 17.6625 C.ar 1 <0> -0.1500
8 C8 -38.3103 -45.1263 19.1185 C.ar 1 <0> -0.1500
9 C9 -34.3860 -45.1685 17.1591 C.ar 1 <0> 0.0730
10 C10 -36.7949 -44.7298 17.1593 C.ar 1 <0> 0.0000
11 C11 -38.1393 -44.9556 17.7322 C.ar 1 <0> 0.0000
12 C12 -39.5741 -45.3226 19.7058 C.ar 1 <0> -0.1435
13 C13 -40.6942 -45.3723 18.8764 C.ar 1 <0> 0.0825
14 C14 -38.9089 -44.3599 21.9429 C.2 1 <0> 0.8520
15 C15 -37.9597 -46.3841 22.5163 C.cat 1 <0> 1.2000
16 C16 -41.1683 -45.4225 21.6511 C.3 1 <0> 0.0000
17 C17 -39.7113 -45.4587 21.1987 C.3 1 <0> 0.5321
18 C18 -42.1196 -46.1030 20.6517 C.3 1 <0> 0.2800
19 C19 -43.5659 -45.7880 21.0665 C.3 1 <0> 0.0000
20 C20 -41.9580 -47.6288 20.5967 C.3 1 <0> 0.0000
21 C21 -36.8757 -44.2879 23.4548 C.3 1 <0> 0.3276
22 N1 -32.3619 -46.4147 18.1879 N.1 1 <0> -0.5571
23 N2 -37.8740 -45.0239 22.6896 N.am 1 <0> -0.7373
24 N3 -39.0202 -46.6925 21.6603 N.pl3 1 <0> -0.8443
25 N4 -37.1414 -47.3306 23.0784 N.pl3 1 <0> -0.9667
26 O1 -39.0907 -43.1545 21.8858 O.2 1 <0> -0.5700
27 O2 -41.9721 -45.5649 19.3259 O.3 1 <0> -0.3625
28 H1 -35.1681 -42.8587 14.7998 H 1 <0> 0.1500
29 H2 -33.2151 -44.0515 15.7227 H 1 <0> 0.1500
30 H3 -37.4143 -43.2460 15.6963 H 1 <0> 0.1500
31 H4 -39.2254 -44.8722 15.8552 H 1 <0> 0.1500
32 H5 -41.4267 -45.2195 16.8522 H 1 <0> 0.1500
33 H6 -35.7883 -46.1407 18.4626 H 1 <0> 0.1500
34 H7 -37.4379 -45.0828 19.7693 H 1 <0> 0.1500
35 H8 -41.2733 -45.8652 22.6502 H 1 <0> 0.0000
36 H9 -41.4733 -44.3708 21.7473 H 1 <0> 0.0000
37 H10 -44.2797 -46.2135 20.3518 H 1 <0> 0.0000
38 H11 -43.7432 -44.7059 21.0662 H 1 <0> 0.0000
39 H12 -43.7957 -46.1780 22.0636 H 1 <0> 0.0000
40 H13 -42.7238 -48.0740 19.9503 H 1 <0> 0.0000
41 H14 -42.0466 -48.0773 21.5915 H 1 <0> 0.0000
42 H15 -40.9999 -47.9272 20.1619 H 1 <0> 0.0000
43 H16 -37.3716 -43.7540 24.2692 H 1 <0> 0.0000
44 H17 -36.1260 -44.9651 23.8687 H 1 <0> 0.0000
45 H18 -36.3772 -43.5731 22.7933 H 1 <0> 0.0000
46 H19 -39.2557 -47.6489 21.4089 H 1 <0> 0.4500
47 H20 -36.3777 -47.0801 23.7001 H 1 <0> 0.4500
48 H21 -37.2812 -48.3199 22.8878 H 1 <0> 0.4500
@<TRIPOS>BOND
1 1 9 1
2 1 22 3
3 2 3 ar
4 2 4 ar
5 3 9 ar
6 4 10 ar
7 5 6 ar
8 5 11 ar
9 6 13 ar
10 7 9 ar
11 7 10 ar
12 8 11 ar
13 8 12 ar
14 10 11 1
15 12 13 ar
16 12 17 1
17 13 27 1
18 14 17 1
19 14 23 am
20 14 26 2
21 15 23 1
22 15 24 2
23 15 25 1
24 16 17 1
25 16 18 1
26 17 24 1
27 18 19 1
28 18 20 1
29 18 27 1
30 21 23 1
31 2 28 1
32 3 29 1
33 4 30 1
34 5 31 1
35 6 32 1
36 7 33 1
37 8 34 1
38 16 35 1
39 16 36 1
40 19 37 1
41 19 38 1
42 19 39 1
43 20 40 1
44 20 41 1
45 20 42 1
46 21 43 1
47 21 44 1
48 21 45 1
49 24 46 1
50 25 47 1
51 25 48 1
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