GROMACS topology for retinal

Gromacs topology of a retinal bound to lysine via protonated Schiff base

Here you find the files required to use gmx pdb2gmx to generate a GROMACS topology of retinal bound to lysine via a protonated Schiff base.

These files generate a GROMACS topology of a retinal attached to a lysine, for a simulation using the AMBER99SB*-ILDN force field. Hydrogens may or may not be described as virtual sites. The retinal is in the all-trans state. Note: The image shows an iodo-retinal.

These files come without any warranty of any kind. Check the topology carefully before using it. If you find a bug, please report it to Jochen Hub.

The retinal parameters come originally from Hayashi et al. (see below) and were converted to Gromacs format by Jochen Hub. The AMBER99SB*-ILDN files were take from the Gromacs user contributions in November 2012. If you use these files for publication, please cite (in addition to the AMBER references):

Biophysical Journal, 2011   PDF DOI Supporting Info
Structural Changes during the Formation of Early Intermediates in the Bacteriorhodopsin Photocycle
Biophysical Journal, 2002   DOI
Jochen Hub
Jochen Hub
Professor of Computational Biophysics