On Tue, Jun 04, 2024, Hantz, Eric via AMBER wrote:
>
>
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-C12-C10-*
> +--- With Sp2 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
I'm trying to figure out how you got atoms types C10, C12 and N3. As you
point out, this has nothing to do with small molecules, since GAFF2 atom
types are all lower-case. Are you perhaps using some old force field (in an
"oldff" folder)? Can you show us the entire tleap input where the error
appears?
>addAtomTypes {
> { "C10" "C" "sp3" }
> { "C12" "C" "sp3" }
> { "N3" "N" "sp2" }
> ...
>}
This looks correct, but you need to make sure that this command is executed
before you load a lib file that has these atoms types.
>The topology files of the protein-ligand complex are generated
>from tLeap, but I'm not sure if I can trust the small molecule
>torsions/hybridizations. I have used my workflow for other small molecules
>and have not run into this issue before.
As noted above, this warning (which is in any event probably innocuous,) has
nothing to do with small molecules. But I also don't see the atom types
above in any standard Amber force fields, but I could well be missing
something -- this is why it would be good to see the complete tleap input file.
...good luck...dac
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Received on Tue Jun 04 2024 - 16:00:02 PDT
