[gmx-users] Acetylated histone with DNA

Justin Lemkul jalemkul at vt.edu
Wed Nov 29 14:08:12 CET 2017

On 11/29/17 4:22 AM, Mehreen Jan wrote:
> Hello
> Hope all will be fine
>   I have acetylated the lysine from Vienna PTM server using 54a8 force field. Lysine was successfully acetylated (KAC).I have simulated the acetylated protein by uisng 54a8ff downloaded from Vienna PTM and the expeiment was successful at 1ns. Now we want to simulate acetylated protein with DNA, as there is no combine force field. We modify the amber99bsc1ff by copying the parameters of KAC form 54a8 force feild,we got following error:
>                                  :the atom type CH1 (residue KAC) notfound in atom type database'.
> one more thing if we delete CH1 the acetylated lysine was completely deleted. can any one help me by suggesting me the force field having combine parametres for both.

CHARMM36 can handle this. The acetylated lysine residue is called ALY. 
For some reason, it's not in the GROMACS port of the force field, but 
you can find it in the CHARMM distribution in 
stream/prot/toppar_all36_prot_modify_res.str (RESI ALY). Just create a 
new .rtp entry based on LYS and add it to residuetypes.dat.



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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