AMBER Archive (2009)
Subject: Re: [AMBER] C1, C2 & C3 carbon types in generalized Born implementation igb=5
From: case (case_at_biomaps.rutgers.edu)
Date: Thu Dec 17 2009 - 07:03:27 CST
On Thu, Dec 17, 2009, Nils Jan Daniel Drechsel wrote:
> I am currently in the processing of implementing the generalized Born
> method igb=5 into our molecular simulator, Adun.
> case 6:
> if ( strncmp(sType,"C1",2) &&
> strncmp(sType,"C2",2) && strncmp (sType,"C3",2) )
> dGBrad = 1.7;
> dGBrad = 2.2;
> On the last lines (case 6), different radii are associated with
> different types of carbon. However, C1, C2 & C3 are nowhere to be
> found in the parameter and topology files and I expect their meaning
> to be how many hydrogens are bound to it, or something like that.
> Would one of the developers be so kind to elaborate this association?
> it would be of great help.
C1, C2, and C3 are united atom carbons (carbons with implicit hydrogens
attached). That is why (a) they don't exist in any of the all-atom force
fields; and (b) if found they would be assigned a larger radius than that
used for all-atom carbons.
So, for comparison to all atom calcs, you can ignore C1, C2, and C3 atom
types. [I haven't kept up on how much has been done to check GB calculations
with united atom force fields...that would be in Ray's bailiwick.]
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