Rosetta基础2：preparing ligand

Rosetta是基于残基模块计算，也就是说Rosetta不把原子单独对待，而是把它们看作一个完整的化学实体。为了实现这个目标，Rosetta必须知道键长、键角以及其它性质。对标准残基和小分子残基模型都是必须的。Rosetta在params文件中对残基的性质进行编码。Rosetta数据库包含常见氨基酸残基和小分子残基的parmas文件。当我们添加新的配体时，需要生成新的parms文件。

What is a Params File

params文件包含残基的几何形状和化学特征的信息，为了让Rosetta理解怎样运行这个残基，应该有一个和这个残基相关联的params文件。可在Rosetta/main/database/chemical/residue_type_sets/fa_standard/residue_types 查看标准残基的params文件

Generating the Params File

我在win10上装的openbabel-3-1-1版本，利用open babel生成配体构象簇(conformers)

D:\abc\Chem\Rosetta\prepare-ligand\UNK> obabel UNK.mol2 -O UNK_conformers.sdf --conformer --nconf 30 --score rmsd --writeconformers
Initial conformer count: 30
128 attempts,  35 duplicates, 64 failed filter.
0 0 0 0
0 0 0 6
2 2 1 6
2 0 1 0
2 0 1 11
2 1 1 11
2 1 1 4
2 2 1 4
.........
0 1 0 2
2 2 0 5=====> Starting conformers search with a Genetic Algorithm <=====
Perform elitist generation replacement with mutation only
Mutation probability: 0.2
Will stop after 5 generations without improvement.Generation #1  0.394971
Generation #2  0.394971
Generation #3  0.394971
Generation #4  0.394971
Generation #5  0.394971
Generation #6  0.394971
1 0 2 3
1 0 0 3
1 0 0 6
2 0 0 0
1 1 2 2
.........
2 0 1 1
GetConformers:
1 0 2 3
1 0 0 3
1 0 0 6
2 0 0 0
..........
2 0 1 1
1 molecule converted

当生成 UNK_conformers.sdf，就可利用Rosetta生成params文件

[user@localhost UNK]$ /usr/local/python-2.7.16/bin/python2 $ROSETTA/main/source/scripts/python/public/molfile_to_params.py -n UNK -p UNK --conformers-in-one-file UNK_conformers.sdf
Centering ligands at (  33.159,  123.537,   22.683)
Atom names contain duplications -- renaming all atoms.
WARNING:  structure contains double bonds but no aromatic bondsAromatic bonds must be identified explicitly --alternating single/double bonds (Kekule structure) won't cut it.This warning does not apply to you if your molecule really isn't aromatic.
Total naive charge 0.570, desired charge 0.000, offsetting all atoms by -0.025
WARNING: fragment 1 has 6 rotatable bonds; protein residues have 0 - 4
Average 23.0 atoms (11.0 non-H atoms) per fragment
(Proteins average 15.5 atoms (7.8 non-H atoms) per residue)
WARNING:  no root atom specified, using NBR atom instead.
Wrote params file UNK.params
[user@localhost UNK]$ ll
total 128
-rw-rw-r-- 1 user user 56376 Aug  4 02:29 UNK_conformers.pdb
-rw-rw-r-- 1 user user 65280 Aug  4 02:15 UNK_conformers.sdf
-rw-rw-r-- 1 user user  3233 Aug  4 02:29 UNK.params
-rw-rw-r-- 1 user user  1944 Aug  4 02:29 UNK.pdb

-n：定义配体的名称
-p：定义params文件的名称
查看molfile_to_params.py其他参数：

(base) [user@localhost prepare-ligand]$ /usr/local/python-2.7.16/bin/python2 $ROSETTA/main/source/scripts/python/public/molfile_to_params.py --help
Usage: molfile_to_params.py [flags] { INPUT.mol | INPUT.sdf | INPUT.mol2 }
.......

params文件内容解析：
文件最后一行出现：PDB_ROTAMERS UNK_conformers.pdb，告诉Rosetta配体的params文件的存放位置。params文件成功生成。

(base) [user@localhost UNK]$ cat UNK.params
NAME UNK
IO_STRING UNK Z
TYPE LIGAND
AA UNK
ATOM  C2  CH2   X   -0.20
ATOM  C1  CH2   X   -0.20
ATOM  P1  Phos  X   1.48
ATOM  O1  OH    X   -0.68
ATOM  H1  Hpol  X   0.41
ATOM  O4  OOC   X   -0.78
.....................................
ATOM  H9  Hpol  X   0.41
ATOM  H6  Hapo  X   0.07
ATOM  H4  Hapo  X   0.07
ATOM  H5  Hapo  X   0.07
BOND_TYPE  O1   P1  1
BOND_TYPE  O1   H1  1
BOND_TYPE  P1   C1  1
...............................
BOND_TYPE  C5   H11 1
BOND_TYPE  C5   H12 1
CHI 1  C1   P1   O1   H1
PROTON_CHI 1 SAMPLES 3 60 -60 180 EXTRA 1 20
CHI 2  C3   C4   O2   H7
PROTON_CHI 2 SAMPLES 2 0 180 EXTRA 1 20
CHI 3  C2   C1   P1   O1
CHI 4  C3   C2   C1   P1
CHI 5  C1   C2   C3   C4
CHI 6  C2   C3   C4   O2
NBR_ATOM  C2
NBR_RADIUS 5.927369
ICOOR_INTERNAL    C2     0.000000    0.000000    0.000000   C2    C1    P1
ICOOR_INTERNAL    C1     0.000000  180.000000    1.537659   C2    C1    P1
...........................................................................................
ICOOR_INTERNAL    H9  -118.304686   69.354124    1.012360   N1    C3    H8
ICOOR_INTERNAL    H6  -119.010428   70.595842    1.087616   C3    C2    N1
ICOOR_INTERNAL    H4   121.526683   71.895723    1.090501   C2    C1    C3
ICOOR_INTERNAL    H5   114.865154   70.839308    1.090099   C2    C1    H4
PDB_ROTAMERS UNK_conformers.pdb

Using Params File during the Run

params文件已经生成，运行时需告知Rosetta它在哪里，所以在命令行中添加 “ -extra_res_fa ”选项

-extra_res_fa <path-to-params-file>

生成配体构象簇

在Rosetta中Ligand-docking教程，给出了生成构象簇的软件是BCL、OpenEye’s MOE、CSD Mercury，在线网站是Frog 2.1、DG-AMMOS。我尝试过这5个程序，最好用的是Open Babel，开源免费，操作简单。
参考链接 Preparing-Ligands