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

Iodo-retinal 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. (Topology can be provided upon request.)

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):

Time-Resolved WAXS Reveals Accelerated Conformational Changes in Iodoretinal-Substituted Proteorhodopsin
Erik Malmerberg, Zaid Omran, Jochen S. Hub, Xuewen Li, Gergely Katona, Sebastian Westenhoff, Linda Johansson, Magnus Andersson, Marco Cammarata, Michael Wulff, David van der Spoel, Jan Davidsson, Alexandre Specht, Richard Neutze
Biophys. J. 101, 1245-1353 (2011) [pdf] [www] [supporting info]


Structural Changes during the Formation of Early Intermediates in the Bacteriorhodopsin Photocycle
Shigehiko Hayashi, Emad Tajkhorshid, and Klaus Schulten, Biophys. J. 83, 1281-1297 (2003)

Please check the README.txt in the package for instructions.