On Mon, Aug 05, 2024, Sunanda Samanta via AMBER wrote:
> For the QM/MM simulation of a covalently bound ligand to a Ser
>residue, we considered the Ser-ligand as a modified amino acid (SEN).
>Following Antechamber, the atom type for a sulfur present in the ligand
>part was given as "SO".
>
>ATOM 20 SAR SEN 46 -15.313 1.434 -29.065 2.849000 SO
Can you say what options you gave to antechamber? GAFF(2) atom types are
all lower case. I'm not sure what the line above is showing: it looks like
part of a PDB file(?), but the "SO" is odd. Further, "SO" is not recognized
as a valid atom type for most Amber protein force fields.
Basically, we need to know exactly how you ran antechamber, and all the
commands that you gave tleap to build the input file. It might also help
if you ran parmed and asked for "details" on the atom in question.
The most likely situation is that you have an atom type in your molecule,
but that no corresponding addAtomTypes entry was ever given to tleap to
specify what element atom type "SO" is. That's not a problem for MM
calculations, since the mass is presumably known; but it does cause problems
for QM runs.
....dac
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Received on Tue Aug 06 2024 - 13:30:02 PDT
