---
name: "obrms"
section: "1"
platform: "linux"
package: "openbabel"
version: "3.2.1-1"
release: "Arch Linux 2026-11-01"
platforms: ["linux"]
url: "https://new.carta.tech/obrms"
---

# obrms(1)

Calculate the heavy-atom RMSD between two chemically identical structures

## NAME

**obrms** – Calculate the heavy-atom RMSD between two chemically identical structures

## SYNOPSIS

**obrms** \[-fmxso\] *filename1* *filename2*

## DESCRIPTION

Computes the heavy-atom RMSD of identical compound structures. Structures in multi-structure files are compared one-by-one unless **--firstonly** is passed, in which case only the first structure in the reference file is used.

## OPTIONS

- **-f**, **--firstonly**

  use only the first structure in the reference file (otherwise the n-th molecule in the reference file is compared to the n-th molecule in the test file)

- **-m**, **--minimize**

  Compute the minimum RMSD achievable by applying a rigid-body transformation to the test molecule

- **-x**, **--cross**

  Compute all n^2 RMSDs between molecules of the reference file. Test file is ignored.

- **-s**, **--separate**

  Separate reference file into constituent molecules (disconnected fragments) and report best RMSD

- **-t** *t*, **--timeout** *t*

  Give up on matching after specified number of seconds

- **-o** *file*, **--out** *file*

  Re-oriented test structure output (used with **-m**)

## EXAMPLES

```
obrms ref.sdf test.sdf
```

Calculate the RMSD between ref.sdf and test.sdf. Both files should have the same number of molecules.

```
obrms -f ref.sdf test.sdf
```

Calculate the RMSD between the first molecule in ref.sdf and each molecule in test.sdf.

## SEE ALSO

[obfit(1)](/obfit/1.md).

The web pages for Open Babel can be found at: \<**https://openbabel.org/**\>

## AUTHORS

Open Babel is developed by a cast of many, including current maintainers Geoff Hutchison, Chris Morley, Michael Banck, and innumerable others who have contributed fixes and additions. For more contributors to Open Babel, see \<**https://openbabel.org/docs/Introduction/thanks.html**\>

## COPYRIGHT

Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.\
 Some portions Copyright (C) 2001-2007 by Geoffrey R. Hutchison and other contributors.

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation version 2 of the License.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.