Dear all, I am trying to adapt to Gromacs the parameters of acetylated lysine from 2 sources.
First from http://ares.tamu.edu/FFPTM/ This webpage gives parameters in AMBER format. I've created a new residue in aminoacids.rtp coying the data from the Amber file. The Amber file contains the following impropers: IMPROPER CA H N -M CH CE NZ HZ CH3 NZ CH OH CA O C +M Which I translated in aminoacids.rtp to: [ impropers ] -C CA N H CH CE NZ HZ CH3 NZ CH OH CA +N C O I guess that is correct. The second source is this paper: http://www.cell.com/biophysj/fulltext/S0006-3495(08)70325-4 It reports the point charges but states: " The partial charges are summarized in Table 1 . The backbone torsion parameters are the same as those of the natural lysine residue in the ff03 force field." My question is the following: does that mean that I should not include the previous impropers for this parameterization? After all, the residue topology and atom types are the same as before... All the best, Ramon -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
