Dear Sir/Madam,
Based on literature and tutorial in AMBER webpage, I found GBSA parameters are as follows in general:
.GBIGB 2GBSA 1SALTCON 0.15EXTDIEL 80.0INTDIEL 1.0SURFTEN 0.0072SURFOFF 0.0000
What is the physical meaning of EXTDIEL and INDIEL and SURFTEN and SURFOFF in GBSA calculations? Is the numbreer used above acceptable in general?
To assume the protein is in water, it seems EXTDIEL=80 is quite reasonable. How about INDIEL, why it is 1? Does it mean that we have to assume the protein inside is located in vaccum (where dielectric constant =1) Should this number change for different types of molecules, e.g. a protein with a large number of ARG or a DNA strand?
When should we use SURFOFF and SURFTEN ?
I have tried to read the manual, but I still cannot figure it out. Could you mind to give me some more guidance, e.g. references or basic information?
Best regards,
Catherine
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Received on Tue Aug 09 2011 - 11:00:03 PDT
