I'm using CHARMM-GUI to build a membrane for a crystallized protein that have a co-crystallized cholesterol. I did not have any problems with the protein, but CHARMM-GUI generated an empty parameter file for the cholesterol molecule:
* Parameters generated by analogy by
* CHARMM General Force Field (CGenFF) program version 0.9.7 beta
! Penalties lower than 10 indicate the analogy is fair; penalties between 10
! and 50 mean some basic validation is recommended; penalties higher than
! 50 indicate poor analogy and mandate extensive validation/optimization.
I intend to use these files for namd simulations so I need a proper parameter file. How can I obtain such file?