On Mon, Jul 10, 2017, Robert Wohlhueter wrote:
> FATAL: Atom .R<CALA 348>.A<HN 12> does not have a type.
> FATAL: Atom .R<CALA 348>.A<OT1 13> does not have a type.
> FATAL: Atom .R<CALA 348>.A<OT2 14> does not have a type.
Some part of the toolchain is failing to convert CHARMM atom names like
NH, OT2 and OT2 into PDB-standard names (in this case H, O and OXT). I've
not used the CHARMM-GUI much myself, so maybe others can help out. The
simplest solution may be to just change the atom names in the PDB file using a
text editor.
> ATOM 5461 OT1 ALA 348 -10.021 -0.363 -36.336 1.00 0.00 PROA
> ATOM 5462 OT2 ALA 348 -9.323 -1.620 -38.035 1.00 0.00 PROA
Again, above are non-standard "pdb" files, probably only useful for CHARMM.
Just change OT1,OT2 to O,OXT. But there may be other problems lurking, since
CHARMM uses a lot of nonstandard atom names for proteins. (FWIW: Amber tries
hard, but not completely successfully, to follow the PDB standard for ATOM
and HETATM records. CHARMM emphasizes backwards compatibility with earlier
versions of its program, and ends up with nomenclature that goes back about 35
years, and which was non-standard even then.)
I hope someone on the list knows more than I do about CHARMM-GUI output can
suggest a general way to convert CHARMM-like pdb files into files that follow
the PDB (and Amber) standards.
....dac
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Received on Mon Jul 10 2017 - 19:30:04 PDT
