Re: [AMBER] problem during MD process

From: 蒋峻峰 <>
Date: Wed, 15 Dec 2010 17:38:26 -0800 (PST)

Dear Dean Cuebas!

Thank you for your kindess suggestions! I will try vina as soon as possible to get the complex structure

        J.F. Jiang

发件人:Dean Cuebas
发送日期:2010-12-16 02:13
收件人:AMBER Mailing List
主题: Re: [AMBER] problem during MD process

> From: 蒋峻峰 <>
> Reply-To: AMBER Mailing List <>
> Date: Sun, 12 Dec 2010 20:09:16 -0600
> To: AMBER Mailing List <>
> Subject: [AMBER] problem during MD process
> 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

I would try Vina for docking... It is blazingly fast and has worked wonders
for me! Don't forget to include the CoA in the protein structure when you do
the docking for your other substrate. Also don't forget that the complex
with both substrates bound could be significantly different than the
enzyme-CoA structure, and you might need simulated annealing to ultimately
get the correct ternary complex structure.


>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
>           2010-12-13
AMBER mailing
> list

AMBER mailing list
AMBER mailing list
Received on Wed Dec 15 2010 - 18:00:02 PST
Custom Search