On Thu, May 18, 2017, Jerrano Bowleg wrote:
To add to Bill's good response:
> FATAL: Atom .R<DT5 1>.A<P 31> does not have a type.
> FATAL: Atom .R<DT5 1>.A<OP1 32> does not have a type.
> FATAL: Atom .R<DT5 1>.A<OP2 33> does not have a type.
> FATAL: Atom .R<DT5 1>.A<OP3 34> does not have a type.
The 5' residues in the Amber library don't have a terminal phosphate group.
> FATAL: Atom .R<DT 10>.A<N9 33> does not have a type.
> FATAL: Atom .R<DT 10>.A<N7 34> does not have a type.
You atom naming scheme for thymine is pretty odd: a pyridmidine would
ordinarily not have N9 and N7 atoms.
> FATAL: Atom .R<DA3 23>.A<'HO3 34> does not have a type.
You want this atom to be HO3', not 'HO3.
You'll need to edit your PDB file to have the atom names match those
in the library. As Bill suggested, the "desc" command in leap can help out.
....dac
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Received on Thu May 18 2017 - 19:30:02 PDT
