[gmx-users] how to creat new.rtp for acetylated lysine (ALY)

Justin Lemkul jalemkul at vt.edu
Mon Dec 4 15:25:14 CET 2017

On 12/4/17 5:27 AM, Mehreen Jan wrote:
> HI!
> Hope you all will be fine.
> Version : Gromacs5.1.4
> Thank you for your reply. According to your advice I have pasted parameters for acetylated lysine (ALY) from “stream/prot/toppar_all36_prot_modify_res.str (RESI ALY)” in the Charmm36ff (merged.rtp). As you suggested that just create a new .rtp entry based on LYS and add it to residuetypes.dat.  Can we rename merged.rtp with new .rtp? How to create new.rtp? Can we add ALY as protein in   residuetypes.dat?   When we past ALY parameters in merged.rtp gives the following error
>                                                                  :at line ALY error *.
> I have removed these asterisk (*) but it gives the following error:
>                                                      : in .rtp file in residue ALY at line
>                                                            : Atom N NH1 -0.47 !.
> Would you like to please tell me how these parameters should be integrated in any force field or in Charmm36 that

You can't simply copy and paste from a CHARMM RTF into a GROMACS .rtp 
file and expect it to work. The format is entirely different.

Look at standard LYS and see how it is formatted. Copy its entry, modify 
as needed, and keep it in the same .rtp file (no need for more .rtp 
files, just write a new residue entry in the existing file).



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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