[gmx-users] GB Parameters

[David van der Spoel]

On 2010-08-23 19.27, Elizabeth Ploetz wrote:
> Dear Gromacs Users,
>
> I am interested in implementing implicit solvent using the OBC GBSA method.  In the Gromacs 4.5beta3 top directory, several force fields (oplsaa and multiple versions of amber) contain the gbsa.itp file, and one (charmm27), contains a gb.itp file.  They all have the same column titles (sar, st, pi, gbr, and hct).  I have read the six articles listed at http://www.gromacs.org/Documentation/Terminology/Implicit_Solvent, however I still have the following two questions regarding the contents of this file:
>
> (1.)  What values are tabulated in these columns and what are the corresponding references for each of them?
> (2.)  Which columns are used (versus ignored) by Gromacs in the implementation of each of the methods (Still/HCT/OBC)?
>
> Here are my guesses for Question 1:
> (a.)  sar: solvent accessible surface area?
> (b.)  st: surface tension?
> (c.)  pi: ?
> (d.)  gbr: generalized born radius?  These values correspond to sigma/2 from Jorgensen and Tirado-Rives' 1988 JACS paper (v. 110, p. 1657).  However the generalized born radius is equal to Rvdw plus a dielectric offset distance, according to Still et al's 1997 J. Phys. Chem. A paper (v. 101, p. 3005).  This would mean the dielectric offset distance is set to zero (?).
> (e.)  hct: HCT parameter
>
> With an eventual goal of implementing implicit solvent using my lab's force field, insight into the meaning of the columns and/or references for their origin would be greatly appreciated.
>
> Thanks in advance!
>
> Sincerely yours,
>
> E. A. Ploetz
Hi Elizabeth,

I can not answer your question, but it is very good that you are 
scrutinizing this stuff, since it is new code...

Does your lab's force field include support for nucleic acids? This is 
missing from the current Charmm implementation although there are 
rumours that parameters exist.


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se