On Mon, Mar 06, 2017, Nikolay N. Kuzmich wrote:
> FATAL: Atom .R<ADF 630>.A<N 35> does not have a type.
> FATAL: Atom .R<ADF 630>.A<C 36> does not have a type.
Just to make this more explicit: your pdb file has atoms named "N" and "C"
in the ADF residue, but the ADF residue you defined doesn't have such
atoms--I'm guessing they might called "N30" and "C32" in the library...
> FATAL: Atom .R<CPRO 766>.A<O1 16> does not have a type.
> FATAL: Atom .R<CPRO 1494>.A<O1 16> does not have a type.
Same idea: the oxygens in any C-terminal residue are called "O" and "OXT",
but it looks like your structure calls one of them "O1".
You must edit the structure (PDB) file so that the atom names match those
in the libraries.
> HETATM23306 N ADF A 630 6.272 -4.170 -4.285 1.00
> HETATM23308 C ADF A 630 7.111 -1.871 -3.989 1.00
Above atoms are indeed in the PDB file, but not in the library you created
for this residue.
>
> ATOM 11636 O1 PRO A 766 15.304 -22.458 -23.180 1.00
This atom should probably be called "OXT", not "O1".
Please remember that LEaP is just a bookkeeping program: it matches atoms and
residues in your PDB file with atoms and residues in your libraries.
....dac
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Received on Mon Mar 06 2017 - 19:00:02 PST
