forked from yuedongyang/DLIGAND2
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathREADME.md
44 lines (40 loc) · 1.38 KB
/
README.md
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
# DLIGAND2
DLIGAND2 is a knowledge-based method to predict protein-ligand binding affinity based on a distance-scaled, finite, ideal-gas reference (DFIRE) state.
<div style="align: center">
<img src="https://github.com/TH-CADD/DLIGAND2/blob/master/doc/picture.png" width="70%" div align=center />
</div>
# How to run
When you have downloaded the DLIGAND2 software package, the following files can be obtained:
```
$ tree
.
|-- bin
| |-- amino.mol2
| |-- dfire.2
| |-- dligand2.gnu
| |-- dligand2.intel
| `-- Potential_parameters.txt
|-- doc
| `--pitcure.png
|-- example
| |-- 966c_ligand.mol2
| |-- 966c_protein.pdb
| `-- run_example.sh
|-- LICENSE
`-- README.md
2 directories, 9 files
```
Two version of executable dligand2 are provided, the envrionment of DATAPATH must be set to find the files of amino.mol2 and dfire.2. Then:
```
$ cd example
$ ../bin/dligand2.intel
Usage: ../bin/dligand2.intel [-v] [-s dfire.2] [-etype 1,2] [-P protein] [-L ligand]
$ ./dligand2.intel -etype 1 -P ../966c/966c_protein.pdb -L ../966c/966c_ligand.mol2
-12.4143
$ ./dligand2.intel -etype 2 -P ../966c/966c_protein.pdb -L ../966c/966c_ligand.mol2
-13.908
$ ./dligand2.intel -P ../966c/966c_protein.pdb -L ../966c/966c_ligand.mol2
-12.4143
```
The argument of [-etype 1,2] gives two versions of potentials,represents the atom type in protein subdivided into 167 atom types and 13 atom types.
Enjoy!