AMBER Archive (2006)

Subject: Re: AMBER: helices in GB simulations

From: Carlos Simmerling (
Date: Mon Nov 27 2006 - 12:12:02 CST

we and others have shown that some of the GB models overstabilize helices,
although I have not used igb=2 (only 1,5,7). I will say that you get
more helix but the helices are poorer geometry, so that some programs that
are rigid in requirements for the H-bonds for example may say that you
have less helix. Make sure to check more than just H-bonds.
The GB models indeed have weaknesses, you should make sure
to read the literature on that carefully before using the GB models.
This seems to be particularly important for simulations of small peptides
that are often only marginally stable in the best case.

another thing to consider is timescale- it may well be that the protein
force field
you are using is of poor accuracy, and the GB model will just show the
changes more quickly than in the higher viscosity explicit water.
In order to know if it is the protein parameters or the water model you
really need to separate the issues of timescale and thermodynamic

Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail:
Stony Brook, NY 11794-5115

Marie-Pierre Durrieu wrote:

> Dear all,
> I have done a GB simulation (with the option igb=2) and a water
> simulation on a long helicoidal system. According to experiences my
> protein is very stable, so I expect the alpha helices not to deform
> too much during simulations.
> The trouble is the GB simulation loses almost 50% of the (n,n+4)
> hydrogen bonds present in the water simulation. Is it alarming ? Is GB
> known for destructuring alpha helices ? Or is GB only exploring more
> conformational space ?
> Thanks in advance,
> Marie-Pierre.

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