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
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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