On Thu, 2013-10-31 at 16:20 -0400, Adrian Roitberg wrote:
> Hi All,
>
> I found a peculiar behavior that I need help solving.
>
> 99SBildn has created some new atom types that seems to conflict with
> other names. In particular, ILE has a new C3 type, associated with the
> CG2 carbon atom.
>
> Tleap assign that CG2 as C3, and if one uses GB, it assign a value of
> the Born radii of 2.2, clearly too large.
>
> Same exact setup with ff99SB, assigns a CT type to CG2, and a born radii
> of 1.7
>
>
> The conflict seems to be with C3 atom names being present in some
> version of the UA FFs and also in nucleic acids.
As an update, the consensus was that C1, C2, and C3 historically
referred to united atom CH, CH2, and CH3 groups, respectively. As a
result, they were assigned larger GB radii, as you would expect.
I added code to tleap to try and determine if C1, C2, and C3 atom types
were in fact UA carbons by looking at their respective masses. Any
C1/C2/C3 atom type with a 'normal' carbon mass is now assigned a radius
of 1.7 A instead of 2.2.
This is a temporary solution that should work fine until a more
permanent solution is decided upon and implemented. [1]
All the best,
Jason
[1] Which likely means it will be a permanent temporary solution :)
P.S. -- Should this be made into an update? The code itself is
remarkably simple (16 lines; mostly comments)...
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Nov 04 2013 - 12:30:02 PST
