[gmx-users] simulating the effect of Ph

[Justin A. Lemkul]

Bharath.K. Chakravarthi wrote:
> hello all...
> i know simulating the effect of temperature and pressure on the protein....
> is there any way to study the effect of Ph on the system....
> 

That is a complex question, but there are a number of useful discussions about 
this in the list archive.  The short answer is "not really," but you may be able 
to derive some useful information from altering the protonation state of certain 
residues in your protein structure using the interactive options of pdb2gmx. 
Some other useful information:

http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation

-Justin

> 
> -- 
> Bharath.K.Chakravarthi
> Ph:9535629260
> 

-- 
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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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