VMD-L Mailing List

From: Rune Thomas Kidmose (rtk_at_biomed.au.dk)
Date: Mon Feb 18 2019 - 13:22:17 CST

Hi everyone,

I would like to turn your attention to a small web service we have made available at Aarhus university, called Namdinator.

Namdinator is an easy-to-use tool that enables users to run a Molecular Dynamics Flexible Fitting (MDFF) simulation in an automated manner through a pipeline system, which we are hosting on our web server for free. All you need to do is upload your map (mrc format in P1 spacegroup), the model you want to fit and state the resolution of the map and hit "submit job". NB. the model should be rigid-body fitted (COLORES, chimera fit-to-map etc.) into the target map before uploading the files!

To automate the MDFF simulation process, some compromises had to be made, the largest being that all HETATM's records are automatically stripped from the input PDB file, meaning that no ligands, glycosylations, ions, water molecules etc. are included in the simulation and hence not in the output PDB files. This should be kept in mind, if relevant, when analysing the results from Namdinator.

After the MDFF simulation is done, the output model is piped through a standard phenix.real_space_refine run to fix most of the model errors introduced in the simulation.

The input and output files are run through some standard validation programs and the results are summarized at the end of the run. All of the models can be visually inspected in a NGL-viewer after the run is finished.

If you would like to know more, please read our bioRxiv paper: https://www.biorxiv.org/content/10.1101/501197v1

Otherwise, please visit https://namdinator.au.dk/ to give it a try!!! As a test case I would recommend you to simply use the EMDB/PDB pair suggested on the "Fetch" tab (6640/3JD8 resolution 4.4Å) using the default settings.

I should note that we, of course, did not invent or develop MDFF, we have simply made an automated pipeline for running MDFF. Also we can not access your data, so dont worry about uploading unpublished results etc.

Feel free to comment on likes/dislikes/improvements and report any bugs directly to me!

Cheers

Ruki