[gmx-users] Re : Protein carbohydrate simulation

[Justin A. Lemkul]

bharat gupta wrote:
> Hi all,
> 
> I am interested in studying the interactions between the Sulf2 protein
> (endosulfatase) , which I have modelled and its substrate hearan
> sulfate . Can anybody help me to carry out such type of simulation
> studies ..
> 
> Please reply ASAP
> 

Not until you can prove that you've actually done your homework.  This forum is 
not the place to get step-by-step instructions on how to set up and run a 
simulation.  Several useful references:

1. Protein-ligand tutorial on the Gromacs site:
http://www.gromacs.org/Documentation/Tutorials

2. Parameterization of your substrate (which is a very difficult topic, suitable 
for only experienced users):
http://www.gromacs.org/Documentation/How-tos/Parameterization

3. Literature.  Surely you're not the first person who wants to study a 
protein-carbohydrate interaction; there are likely published protocols.

Your biggest challenge is #2; ask yourself whether or not you're up to the task 
of deriving parameters if none are already available.  If you have reliable 
parameters, the simulation is hardly different from a basic MD run.

-Justin

-- 
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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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