[gmx-users] MM/PBSA Gromacs

[R.S.K.Vijayan]

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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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