On Tue, Feb 19, 2019, Keiran Corbett wrote:
>Beginning GB calculations with /apps_shared/amber/amber14/bin/sander
> calculating complex contribution...
> bad atom type: i
>
>I was just checking that this was due to iodine being in my ligand or if
>anyone was aware of a work around?
>
Background: GB calculations require a "dielectric radius" (aka Born
radius) for each atom. But Amber developers only developed parameters
for proteins and nucleic acids, and not for all general organic
molecules. Hence, parameters for things like Br or I are not available.
You can get workarounds by searching for "amber bad atom type" on Google
or some similar search engine. Here is a good link:
http://archive.ambermd.org/201111/0370.html
Do the same thing for I that Jason suggests for Br. You may want to do
more searches to see what radius others have used.
[Usual comment about upgrading: this problem *may* have been solved in
more recent releases, which now store GB radii in the prmtop file. I
don't know when that practice began....so consider, for many reasons, an
upgrade AmberTools18.]
....dac
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Received on Wed Feb 20 2019 - 18:30:02 PST
