AMBER Archive (2004)

Subject: RE: AMBER: how to deal with the initial structure?

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Aug 23 2004 - 21:19:23 CDT

Hi Hjzou,

> differences between apo- and holo- system.However,no crystal
> structure of apoprotein is available so far.So I wanna delete
> the ligand of holo-protein,take it as the initial structure
> of apoprotein and then perform a long-time simulation.Can
> anyone tell me whether it's reasonable or not? Any other suggestions?

I would try it and see what happens. It is probably as reasonable as trying
to predict a structure via other methods. You may need to take a look and
see if the cavity left behind by removing the ligand is solvent accessible.
If it is you may need to add some waters to the cavity. The problem is by
removing the ligand you create a vacuum bubble in its place. This could
cause problems when you start simulating. If you fill it with your solvent
this might help (but if the cavity is not solvent accessible then this might
not be a good idea.). You will also probably need to carefully minimise your
system before you start MD. And also probably let it relax at a low
temperature 50 - 100K before you heat it up fully. In this way any large
forces created by removing the ligand will not cause your system to "blow
up". Then I would proceed with quite a bit of equilibration at 300K in order
to allow structural changes to occur.

I hope this helps. I often find that in these situations the best thing to
do is to try it out and see if you get something reasonable. At least since
these are computer simulations you don't run the risk of blowing yourself up
;-).

All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

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