[gmx-users] Parameterizing Acetylated lysine: need for impropers?

[Ramon Crehuet]

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