GBSAObc setup question

[Siddharth Srinivasan]

I am trying to lay around with the implicit solvent model, and have a few questions about the specific parameters in the API

1. To get the radii, we need to obtain this from some file containing a mapping between AMBER atomtypes and radii. In the Gromacs example, there is a params.agb file that has this mapping. But for a non-Gromacs application, how would I go about getting these radii? I assume that in this params.agb file the "amber99_0, amber99_2" are codes for AMBER atomtypes. Is there a reference I can use to get these values for my application?

2. For the scale factors, it seems like the mapping is
{{{
H = 0.85
C = 0.72
N = 0.79
O = 0.85
S = 0.96
}}}
Is this standard for all atom AMBER?

[Mark Friedrichs]

Hi Siddharth,

My understanding is that the OBC parameters (radii in the params.agb file and the hardwired scale factors in Gromacs-OpenMM) are based on Amber force-field parameterizations. We have radii for protein atom types for Amber94 and Amber99 -- I can pass these on if it would help. The scale factors are the same for these two force fields. If you are using a different (i.e, non-Amber) force field, then these parameters may not be appropriate. I will check w/ members of the Pande group to see if any of them are aware of other OBC parameters sets.

Mark

[Siddharth Srinivasan]

Thanks for the reply, Mark. I am using the standard Amber99 force field, so if you can pass the radii sets to me, or point me to the reference, that would be excellent. My email is sshrinivasan@gmail.com, or this forum thread is fine too.