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
--
========================================
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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