Hi, > It would probably be easier, faster, and more accurate to just use most of > the parameters for Cys rather than try to have PRODRG re-create a > (potentially flawed) model of your compound. The only new parameters are > related to SO3, so the rest should be identical to the Cys residue.
That's not a good idea. It'll only do for the backbone. The charge of CB will be quite different, as well as the CA-CB-SG angle, and for the rest there's nothing similar even. > This is where parameterization becomes a chore - when there's nothing > analogous to what you're doing. Proper Gromos96 parameterization > methodology would dictate that you generate an analogous compound (i.e., > methyl sulfonic acid) and adjust its parameters such that it reproduces > various condensed-phase thermodynamic and physical properties (DeltaG of > solvation, liquid density, heat of vaporization). Proper derivation is > quite time-consuming. Perhaps someone has already done this work and it is > published. If you're unlucky, you've got to do it all yourself. That's a good idea :) Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
