On Mon, Feb 26, 2024, Sasha Buzko via AMBER wrote:
>Thank you for your suggestion to use CYX as the branching point. I have the
>parameters for the linkers (from antechamber) and tleap is not complaining
>about the branching. However, it gives an error message when checking the
>structure:
>Error: Could not find angle parameter: S - CT - C
>
>Error: Could not find angle parameter: S - CT - HC
>
>Error: Could not find angle parameter: S - CT - HC
>
>Looks like it's having trouble with the bonds around the sulfur in the CYX
>residue. I have loaded gaff and gaff2 but it still gives this error. Can
>you think of a way to get around this?
Atom types using upper case letters (as above) are for Amber atom types.
GAFF used lower case letters for atom types, so loading those files won't do
you any direct benefit. But you could look in gaff2.parm for similar angles
(just changing upper to lower case): then make a frcmod file with the
upper-case equivalents.
Or, you may just wish to change the atom types above. Methionine in Amber
force fields has S-CT-H1 (instead of S-CT-HC). I don't know the chemistry
involved in your linker, but amino12.lib (used for ff19SB) has 2C-2C-S,
which may be close to what you need.
The "general" problem is that antechamber is mainly used for non-covalent
ligands. If you want to link to an amino acid, you probably want (as you
are doing) to use Amber atom types. But then you need to be inventive to
find missing angle parameters. You can generally check what you decide upon
by minimizing the system, and looking carefully at the resulting geometry
around you new chemistry.
...hope this helps...dac
p.s. sorry to insert myself into this conversation. Dr. Horn may have more
specific advice here.
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Received on Mon Feb 26 2024 - 15:00:02 PST
