simulating Acetylated lysine substrate complex

Date: Sun Nov 14 2010 - 23:12:11 CST

Hi there,

Good Day!

I need to carry out a simulation of a protein that has an acetylated lysine as substrate [ALY] and the ACE group [product] as a part of the pdb file. I tried generating the psf file but, it shows unknown residue ALY and ACE. Although, i added a topology file ACE generated through the swissparm site, i get the same error. FYI, I used the top_all27_prot_lipid topology file for psf generation.

Any suggestions would be greatly appreciated,


Subha Kalyaanamoorthy,
PhD Researcher,
Department of Computer Science and Computer Engineering,
La Trobe University,
Bundoora, Australia.

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