[AMBER] problem during MD process

From: 蒐飾桁 <asakiayumikio.gmail.com>
Date: Sun, 12 Dec 2010 18:09:16 -0800 (PST)

Hi everybody,
I am doing a project of acetyltransfer of ACO. The structure including an enzyme, a substrate and a co-enzyme A. This complex was obtained by merging the substrate into the original pdb structure containg the enzyme and ACO. After minimizatin and heat and density process, the rmsd of the whole structure remained less than 0.5, which was perfectly for me to continue the production stage. But after 1ns simulation, i found that the distance between atom lysine NZ and carbon of the ACO, which changed from 3 angstrom to 5, and this trend is more obvious after 2ns' simulation.

So, i fix some hydrogen bond network of lysine NZ and the carbon atom of the ACO. Stilly, the rmsd of the whole structure turned larger than 2 after 4ns simulation. And this could be much more larger if i turn off the restrains.

So, if anybody here could offer some suggestion about how to solve this problem, I am very glad to receive the send back.

PS: the ZDOCK modelling in DS was used to dock the substrate into the protein but none appropriate sturcture was obtained so i extract the substrate from the other which was structurally homology to my complex and merge into the target protein. And some minimization was carried out before load into amber.

        J.F. Jiang
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Received on Sun Dec 12 2010 - 18:30:02 PST
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