# meta HADDOCK

**Repository Path**: quantaosun/meta-haddock

## Basic Information

- **Project Name**: meta HADDOCK
- **Description**: 基于元动力学的 ensemble docking
1. 普通动力学
2. 元动力学
3. 普通动力学ensemble docking
4. 元动力学 ensemble docking
5. 比较
6. 最终结果是使用空载apo靶点实现了holo负载靶点的一个类似诱导契合对接的过程。

- **Primary Language**: Shell
- **License**: Not specified
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 1
- **Created**: 2022-02-16
- **Last Updated**: 2022-02-17

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

# meta HADDOCK

[教程链接](https://www.bonvinlab.org/education/biomolecular-simulations-2018/Metadynamics_tutorial/)
[教程链接2，练习文件由此下载](https://www.bonvinlab.org/education/biomolecular-simulations-2019/Metadynamics_tutorial/)

### First Error


```
gmx grompp -f em-pbc.mdp -c apo-solv-init.gro -o em-pbc.tpr -p apo-solv.top 
                       :-) GROMACS - gmx grompp, 2021 (-

WARNING 1 [file apo-solv.top, line 24004]:
  The GROMOS force fields have been parametrized with a physically
  incorrect multiple-time-stepping scheme for a twin-range cut-off. When
  used with a single-range cut-off (or a correct Trotter
  multiple-time-stepping scheme), physical properties, such as the density,
  might differ from the intended values. Since there are researchers
  actively working on validating GROMOS with modern integrators we have not
  yet removed the GROMOS force fields, but you should be aware of these
  issues and check if molecules in your system are affected before
  proceeding. Further information is available at
  https://redmine.gromacs.org/issues/2884 , and a longer explanation of our
  decision to remove physically incorrect algorithms can be found at
  https://doi.org/10.26434/chemrxiv.11474583.v1 .

Analysing residue names:
There are:   351    Protein residues
There are: 15961      Water residues
There are:     6        Ion residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Number of degrees of freedom in T-Coupling group rest is 106944.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 80x72x64, spacing 0.113 0.113 0.115

Estimate for the relative computational load of the PME mesh part: 0.25

This run will generate roughly 4 Mb of data

There was 1 warning

-------------------------------------------------------
Program:     gmx grompp, version 2021
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2382)

Fatal error:
Too many warnings (1).
If you are sure all warnings are harmless, use the -maxwarn option.

For more information and tips for troubleshooting, please check the GROMACS
```
 

### 
Second error 


```
(base) q@q-ASUS-TUF-Gaming-A15-FA506QM-FA506QM:~/Desktop/metaHADDOCK/MD/plain$ gmx grompp -f equil-pbc.mdp -c em-pbc.gro -p apo-solv.top -n apo-solv.ndx -o em-pbc.tpr 
                      

  gmx grompp -f equil-pbc.mdp -c em-pbc.gro -p apo-solv.top -n apo-solv.ndx -o em-pbc.tpr

WARNING 1 [file apo-solv.top, line 24004]:
  The GROMOS force fields have been parametrized with a physically
  incorrect multiple-time-stepping scheme for a twin-range cut-off. When
  used with a single-range cut-off (or a correct Trotter
  multiple-time-stepping scheme), physical properties, such as the density,
  might differ from the intended values. Since there are researchers
  actively working on validating GROMOS with modern integrators we have not
  yet removed the GROMOS force fields, but you should be aware of these
  issues and check if molecules in your system are affected before
  proceeding. Further information is available at
  https://redmine.gromacs.org/issues/2884 , and a longer explanation of our
  decision to remove physically incorrect algorithms can be found at
  https://doi.org/10.26434/chemrxiv.11474583.v1 .


-------------------------------------------------------
Program:     gmx grompp, version 2021
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 681)

Fatal error:
number of coordinates in coordinate file (em-pbc.gro, 51622)
             does not match topology (apo-solv.top, 51610)

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

```