[gmx-users] Energy minimizations with gmx3.2

Alan Wilter Sousa da Silva alan at lac.inpe.br
Sun May 23 02:01:23 CEST 2004

I have done what you said to NMR (PR-HIV PDB 1BVE).  And that was fine 
(~70% in region 1).

I can also say that, no matter degree of optimisation, average rama 
throughout trajctories (after termalisation etc.) converges to 70%, 
being the original PDB a crystal (which usually start from >90%)  or NMR 
  (already around 70%).

Nice weekend dear Dr. van der Spoel.


PS: I'm wondering if you'll see this e-mail during Sunday dawn :-)

David wrote:
> On Sat, 2004-05-22 at 19:30, Alan Wilter Sousa da Silva wrote:
>>Hi David!
>>(OT: When do you take a brake? :-)
> No comment...
>>We have worked with others MD programmes too and it seems to happen
>>I use Gromos96 (thus, IIRC, it happens to G87).  No matter PDB file I
>>took, if I did a super EM, I get visible changes.  But rama can show
>>I use procheck.  Procheck define 4 regions:
>>1- Most favoured (A, B, L, red)
>>2- additional allowed (a, b, l, yellow)
>>3- generously allowed (~a, ~b, ~l, cream)
>>4- disallowed (white)
>>	 So let me show what I want to point out with next table:
>>	PDB	EM (emtol=100)
>>1-	95,6	89,9
>>2-	 4,4	10,1
>>3-	 0,0  	 0,0
>>4-	 0,0	 0,0
>>The longer EM, the lower will be rama value for 1 (increasing 2).
>>Ok, I think it's fine, as long as I don't have anything going to region 3
>>or 4.  However, anyway, I do not like this.
> Force fields do have systematic errors in that the minimum energy
> structure is not the same as the experimental structure. However, to
> compare fair, you should perform a simulation of the crystal structure
> in a crystal environment. For NMR structures you should compare to the
> entire NMR ensemble and to data.

Alan Wilter Sousa da Silva
Bolsista Pesquisador LAC-INPE
São José dos Campos (SP), Brasil

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