[gmx-users] where are GB parameters stored?

[Justin A. Lemkul]

David Mobley wrote:
> Hi,
> 
> I'm trying to get going with the OBC GB model in Gromacs, at this point 
> just for some test simulations, and I'm using the gaff small molecule 
> force field, which uses nonstandard atom type names (particularly, 
> lowercase). This means that GROMACS isn't finding GB parameters for my 
> atoms. While these should be relatively standard, I need to add them 
> somehow. According to the manual I can do it using this kind of a 
> topology section:
> 
> [ implicit_genborn_params ]
> ; Atomtype  sar     st   pi      gbr hct
> 
> However, I need some reference parameters to look at (that is, I'd like 
> to be able to look at the table of existing parameters). I've been 
> looking through the "top" directory and can't find them anywhere. Can 
> anyone give me a pointer to where they are? Or are they hardwired into 
> the code somewhere?
> 

There should be a gbsa.itp file in each *.ff subdirectory.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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