I'm also trying to model a MMP. What did you do to keep you Ca2+ in
your protein? I'm having the problem that my structural Ca keep flying
out of my protein during a MD run.
Thanks,
Kara Di Giorgio
On Apr 12, 2005, at 6:37 PM, Yong Xu wrote:
> Dear Case and Holger
>
> I perform MM-PBSA calculation on MMP (metalloproteinase) which include
> 2 Zn+ and 2 Ca2+. What confused me is that the result deltaG value is
> not at the same order with experimental deltaG.
>
> the ki value is at the range of 10-1000nm, while my MM-PBSA result is
> as following
> MMPBSA:PBTOT -75 --- -85 kcal/mol
> TdeltaS:TSTOT -18 --- -19 kcal/mol
> so the deltaG_calc is at the range of -55 --- -65kcal/mol.
> from above data (I finished three MD of MMP-ligand systems),
> qualitative correlation can be obtained, but quantitative result is
> very bad.
>
> WHAT I WANT TO KNOW is that
> (1)should I set "protein + 2*ZN + 2*Ca" as receptor (above result is
> from this setting).
> (2)does this large detaG_calc come from large
> Zn2+--ZBG(ZN-bonded-group) electrostatics interaction.
> (in no-bonded model, charge was set as 2+, while in bonded model from
> other paper, charge on ZN is ~0.95 or 1)
> (3) what should be modified in my MM_PBSA calculation with current
> no-bonded model?
>
> {{I am using amber7 and no-bonded model with 2+ charge on metal ions.
> MD simulations were run for 500ps, from ~200ps-500ps, the complex
> system reach equlibrium stage. I also analyzed Zn-His distance and
> some other H-bonds, and found that this complex system is well stable
> with Zn-His coordinate and stable H-BOND between ligand and protein.
> I take 100 snapshots from 300-500ps traj for MM_PBSA calculation.}}
>
> Any reply would be very appreciated!
>
> Best regard!
>
> Yong Xu
> yxu.mail.sioc.ac.cn
> 2005-04-13
>
> ===========================================================
> * Yong Xu
> * State Key Lab of Bioorganic & Natural Product Chemistry
> * Shanghai Institute of Organic Chemistry
> * Chinese Academy of Science
>
> * 354 Feng Lin Road, Xu Hui District
> * Shanghai, 200032, China
>
> * Email: yxu.mail.sioc.ac.cn
> * xuyongch.yahoo.com
> ===========================================================
>
>
>
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Received on Wed Apr 13 2005 - 03:53:00 PDT
