[gmx-users] Force Field for peptides and proteins

[rajat desikan]

On this note, I wanted to ask about simulated unfolding of proteins. I have
a primarily alpha-helical-protein ( about 300 amino acids, 5 alpha helices,
no beta strands) and 3 of its single point mutants. Now, to answer the
question of relative stability, I want to place them in a water bath and
heat them until they unfold. The temperature at which they unfold should
qualitatively tell me which is more stable (the most stable unfolding at
the highest temperature).

I have been wondering which forcefield would be more suitable. I intend to
use simulated heating at a constant rate (simulated annealing option in
.mdp file). Any answers will be greatly appreciated. Thank you.


On Mon, Aug 12, 2013 at 6:29 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/12/13 8:19 AM, Maria Astón Serrano wrote:
>
>> Dear Gromacs users,
>>
>> We would like to know which is the Force Field which is customarily
>> preferred for simulations of peptides and proteins.
>>
>>
> Interestingly, this same question was just asked on the development list,
> although the discussion indeed belongs here.
>
> http://lists.gromacs.org/**pipermail/gmx-developers/2013-**
> August/007016.html<http://lists.gromacs.org/pipermail/gmx-developers/2013-August/007016.html>
>
> There is a wide body of literature on this topic, and it is very
> educational to read through as much of it as you can.  Some force fields,
> like AMBER94 and CHARMM22+CMAP are decidedly too helical, while others
> (Gromos96 53A6 being a good example) tend to understate helices and
> overstate extended configurations.  New parameter sets like AMBER99SB-ILDN
> and CHARMM22* are often used in protein folding studies and seem to do
> quite well.
>
> I think, in the end, it depends to some extent about the scope of what you
> are doing and the protein(s) to be studied.  Even high quality force fields
> that perform well for folded proteins do not necessarily perform well on
> intrinsically disordered proteins or model peptides.
>
> -Justin
>
> --
> ==============================**====================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
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>
> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
>
> ==============================**====================
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-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore