[gmx-users] MM/PBSA Gromacs

[Per Larsson]

Hi!

There is support in gromacs for gb calculations. However, I'm currently investigating some recent reports about  unstable simulations (unfolding proteins), so my advice is to use the code with caution.

Thanks
/Per


30 nov 2011 kl. 20:04 skrev "R.S.K.Vijayan" <biovijayan at gmail.com>:

> Dear Gromacs users
> 
> Is there any script  that does a PB or GB calculation to perform a MM/PB(GB)SA free energy  calculation in Gromacs. Similar to the MMPBSA.py script available in Amber.  I find a similar question raised by a user a couple of years back.  Any successful implementation????
> 
> 
> Vijayan.R  
> 
> 
> 
> On Wed, Nov 30, 2011 at 1:26 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 김현식 wrote:
> Dear Experts,
>  Hi,
>  Is there any tools in gromacs to get "Hydrophobic cores" of protein ?
>  
> 
> I suppose that depends on what your definition is, but in all likelihood no, not directly.  A program like g_sas can give you nonpolar and polar surface areas as well as volumes and surface atoms, which, through crafty use of index groups, may provide you with something useful.
> 
> -Justin
> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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