[gmx-users] Acetylated histone with DNA

Mehreen Jan mehreen_jan1990 at yahoo.com
Wed Nov 29 10:32:18 CET 2017


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.    
thank you in advanced 

Mehreen Jan
from Pakistan

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