[gmx-users] GB Parameters
per.larsson at sbc.su.se
Mon Aug 23 20:41:51 CEST 2010
Also, again, as David said, if you find any errors in the parameters or in the code, please let me know!
23 aug 2010 kl. 20:09 skrev Per Larsson <per.larsson at sbc.su.se>:
> Values in columns 1-3 are not currently used in version beta3. They pertain to more elaborate surface area algorithms, the one from Still et al in particular.
> Column 4 is the Vdw-radii for atom types that are used for computing the Born radii. The dielectric offset is specified in the mdp-file, and gets added to the input radii for the different radii methods.
> Column 5 is the scale factor for the HCT/OBC models. The values are taken from the original HCT reference, as well as the corresponding implementation in Tinker.
> 23 aug 2010 kl. 19:27 skrev Elizabeth Ploetz <ploetz at ksu.edu>:
>> 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
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