AMBER Archive (2009)

Subject: [AMBER] Molecular simulation of a protein using special H2O cluster

From: Rilei Yu (yulaomao1983_at_yahoo.com.cn)
Date: Tue May 26 2009 - 03:20:56 CDT

Dear AMBER users,
 
Now, I am studying the conformation of a special protein in  the speical solvent constituted by cyclic water hexamers. Now, my problem is that I cannot simulate such solvent. After all, the cyclic water hexamer is sustained by hydrogen bond that cannot exist in the normal condition. Can anyone provide me with an approach that can sustain the water clusters-cyclic water hexamers exsting in my system.
 
I am really appreciated for your help!
 
Best Regards,

Rilei Yu

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