Dear Ryan,
If you are using nonstandard residues and other small organic
molecules, your best bet is to use the radi option of 0 (radiopt=0),
i.e. the radii in the prmtop file.
All the best,
Ray
On Thu, Jan 5, 2012 at 9:53 AM, Ryan Pavlovicz <pavlovicz.7.osu.edu> wrote:
> Hi everyone,
>
> I am encountering a radius assignment error when trying to do a static PB
> calculation in Amber9:
>
> PB Bomb in pb_aaradi(): No radius assigned for atom
>
> I have determined that this problem is due to the new atom types created in
> the ff99SBildn force field, namely replacing ASP CG with the C6 type
> instead of the traditional C type, ILE CG2 with the C3 type instead of the
> CT type, LEU CG with the C4 type instead of the CT type, and ASN CG with
> the C5 type instead of the C type.
>
> Is there an easy way to assign the proper Tan/Luo radii to these atoms so
> that improved non-polar solvation interactions may be calculated? I can't
> figure out which file(s) need to modified to sort this out.
>
> Thanks for your help!
>
> (sorry if you received this twice, i think i sent it to the incorrect email
> address the first time)
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Received on Thu Jan 05 2012 - 15:30:02 PST
