---
name: "gmx-anadock"
section: "1"
platform: "linux"
package: "gromacs-data"
version: "2019.1-1"
release: "Debian 10 (Buster)"
platforms: ["linux"]
url: "https://new.carta.tech/gmx-anadock"
---

# gmx-anadock(1)

Cluster structures from Autodock runs

## NAME

gmx-anadock - Cluster structures from Autodock runs

## SYNOPSIS

```
gmx anadock [-f [<.pdb>]] [-od [<.xvg>]] [-of [<.xvg>]] [-g [<.log>]]
            [-xvg <enum>] [-[no]free] [-[no]rms] [-cutoff <real>]
```

## DESCRIPTION

**gmx anadock** *analyses the results of an Autodock run and clusters the* *structures together, based on distance or RMSD. The docked energy* *and free energy estimates are analysed, and for each cluster the* *energy statistics are printed.*

*An alternative approach to this is to cluster the structures first* *using gmx cluster and then sort the clusters on either lowest* *energy or average energy.*

## OPTIONS

*Options to specify input files:*

- **-f \[\<.pdb\>\] (eiwit.pdb)**

  *Protein data bank file*

*Options to specify output files:*

- **-od \[\<.xvg\>\] (edocked.xvg)**

  *xvgr/xmgr file*

- **-of \[\<.xvg\>\] (efree.xvg)**

  *xvgr/xmgr file*

- **-g \[\<.log\>\] (anadock.log)**

  *Log file*

*Other options:*

- **-xvg \<enum\> (xmgrace)**

  *xvg plot formatting: xmgrace, xmgr, none*

- **-\[no\]free (no)**

  *Use Free energy estimate from autodock for sorting the classes*

- **-\[no\]rms (yes)**

  *Cluster on RMS or distance*

- **-cutoff \<real\> (0.2)**

  *Maximum RMSD/distance for belonging to the same cluster*

## SEE ALSO

**[gmx(1)](/gmx/1.md)**

*More information about GROMACS is available at \<http://www.gromacs.org/\>.*

## COPYRIGHT

*2019, GROMACS development team*