AMBER Archive (2008)

Subject: AMBER: About Hydrophobic Interactions.

From: cgji (cgji_at_itcc.nju.edu.cn)
Date: Mon May 12 2008 - 11:14:00 CDT

Dear Amber Users,

I run MD simulation of a 300-residue protein with explicity water.
 Hydrophobic collapse happened on small part of the system afer 10 ns simulation . One important hydrophobic pocket of the protein was blocked due to this collapse. ( the pocket was filled by a ligand during the simulation.)
I am wondering whether hydrophobic interactions was overestimated in my simulation.

Hydrophobic interactions wasn't included in Classical Force Field explicitly.
It is managed by many interactions especially entropy effect.
    
Which part of parameters in force field contribute most to such hydrophobic force ?

Is balance between paramters of WATER and parameters of AMINO ACID important here?

Are there any papers discussing relationship of force field parameters and hydrophobic interactions ?

Thanks for your advise in advance.

Best Regards,

.....jcg

2008-05-12

cgji

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