[gmx-users] minimization quagmire

Mark Abraham mark.abraham at anu.edu.au
Wed Sep 15 14:47:35 CEST 2010

----- Original Message -----
From: abdullah ahmed <abdullah_renk_ahmed at hotmail.com>
Date: Wednesday, September 15, 2010 21:18
Subject: [gmx-users] minimization quagmire
To: gmx <gmx-users at gromacs.org>

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>  Hello everyone, 
> I have a question regarding the results of minimization. I have two structures that are the same except for 2 residues in the core of the structure that have been changed from luecine to  to glycine. The leucine structure is very well packed and the core is hydrophobic. The introduction of two glycines in the center creates a a cavity in this hydrophobic region.
> I had expected the leucine structure to have better(lower) energy after optimization, however, the opposite was true. I have run minimization in vacuum and with water (water enters the cavity) and the structure with glycine has better energy in both cases.

I'm a bit confused about how water can enter a cavity in the core *during* an EM. I presume they were actually placed in the void during solvation, before EM?

Anyway, that's not the real point. What you've observed is that once the structures have reached the neighbourhood of a nearby local energy minimum, the glycine structure is lower in energy. You haven't necessarily found the global minimum, or two minima that correspond to each other in any meaningful sense. Even if you had, there's no particular reason to expect the difference between these energies to correlate with the differences in the free energy of folding of the two proteins (or whatever). The leucine structure might be happy enough to fold, but have some kind of strain that is relaxed by the glycine mutations - but your observations (as stated) are not evidence of this, either.



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