Dear Amber User and Developer,
I am trying to simulate my enzyme inside solvent with substrate inside.
I use acetonitrile, and n-Hexane and also water as a solvent.
When I make acetonitrile as a solvent I've been defined it as :
>> set ACN.1 restype solvent,
since I read in Ambertool 12 page 61, the value for restype are
“undefined”, “solvent”, “protein”, “nucleic”, or “saccharide”
I am also have pNPP (a small organic molecule) as a substrate.
What should I defined this substrate ?
Should I defined as
>>set.1.pNNPP restype solvent ?
>> set.1.pNPP restype undefined ?
What is the best definition for substrate or ligand ?
Thank you
Best regards,
Setyanto Tri Wahyudi
ITB-Indoneisa
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Received on Tue May 07 2013 - 22:30:03 PDT
