Converting NanoEngineer-1 DNA structure design (MMP file) to all-atom PDB file

This service converts a DNA nanostructure in NanoEngineer-1 (MMP format) to an all-atom structure in PDB format. It also generates a PSF file using psfgen 1.6.2 and the CHARMM36 force field for MD simulation using the NAMD package, as well as coarse-grained chickenwire PDB and PSF files. Please see the README file in the output archive for a detailed description of each file.

Requirements for the MMP file:

1. It has to be a DNA nanostructure in MMP format created using NanoEngineer-1. Other structures (Chunks, nanotubes, Crystal) created using NanoEngineer-1 will result in error.

2. Each residue should be assigned with a nucleotide (A, T, C or G). Although they all look the same in NanoEngineer-1, they are different in an all-atom model. You can assign nucleotides by following our tutorial video.

3. Currently, we do not support the conversion of a closed DNA loop. Each DNA strand has to have clear start (5' end) and end (3' end).

There is a known bug in NanoEngineer-1 which sometimes misplace residues of a complex DNA nanostructure in the exported MMP file. So, if your MMP file has met all the requirements, but if failed to convert. It is possible that you caught the bug of NanoEngineer-1. To resolve it, try to open the MMP file with NanoEngineer-1 save it to another filename. Repeat the process for 2~3 times. If the problem is not solved, feel free to contact us.

Here, we provide a DNA triangle for testing.

For the introduction and the basic usage of NanoEngineer-1, please visit our tutorial.

To obtain statistics for our funding agencies, this service collects and stores your IP address, an approximate location derived from the IP address and a timestamp each time a job is submitted. Your email address is not associated with other data collected and is removed from the server once the job completes and an email is sent. Please contact Chris Maffeo ( with questions, concerns or requests regarding privacy.