[gmx-users] Re: Salt bridge on Protein Surface

[Maarten Wolf]

>On Wed, 2004-11-24 at 07:03 +0000, Maarten Wolf >wrote:
>> Hello,
>>  
>> I am doing md simulations on a small peptide in water.
>> These calculations result in a consistent salt bridge on the surface
>> of the protein. 
>> I find this strange, because I allways thought that salt-bridges on
>> the surface are easily solvated, and thus broken.
>> Is this assumption wrong? Or is this force field related? Or something
>> else?  
>The assumption is wrong in the sense the some >saltbridges are stable and
>others aren't. It may have to do with many things, e.g. a >Lys has quite
>a long hydrophobic that likes being packed. Can also >be force field
>related, or to the size of your box or the amount of >counterions...

How might the box size effect the stability of the salt bridge? 

I performed another simulation with a lot of counterions. The whole protein structure changed, but the salt bridge remained there. Can I then say that the protein structure and the number of counterions have nothing to do with it?


>>  
>> Thanks for any help in advance


>> 
>> 
>> MvG Maarten
>> 
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>-- 
>David.
>________________________________________________________________________
>David van der Spoel, PhD, Assoc. Prof., Molecular >Biophysics group,
>Dept. of Cell and Molecular Biology, Uppsala University.
>Husargatan 3, Box 596,          75124 Uppsala, Sweden
>phone:  46 18 471 4205          fax: 46 18 511 755
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MvG Maarten

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