On Mon, Jan 11, 2021, Sam Walsworth (Researcher) wrote:
>
>Yes I have a ligand which it doesn't recognise but it also doesn't
>recognise any atoms in the amino acids. Essentially the entire system
>is being flagged as non-standard by ff99SB. I haven't modified any of
>the amino acid residues in the PDB file so if the atom types are all not
>recognised by AMBER it sounds like I've missed a preparation/cleaning step.
Start simple: just edit your pdb file to have a few amino acids in it, and
run through tleap. If you can't figure out what is happening, post the
short pdb file and the exact commands you gave to tleap. If no atoms are
being recognized, this is likely due to some simple error.
...good luck...dac
p.s. don't use ff99SB unless you have a really good reason for doing so.
It's more than 15 years old, and has some known deficiences. There is a
reason that it has been relegated to the "oldff" (old force field) folder.
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Received on Mon Jan 11 2021 - 09:00:02 PST
