On Sun, Jul 30, 2017, Jerrano Bowleg wrote:
>
> I have attached my PDB files before submitting to leap and also after leap.
There error messages are quite helpful, although maybe somewhat hard to find:
Created a new atom named: P within residue: .R<DT5 1>
Created a new atom named: OP1 within residue: .R<DT5 1>
Created a new atom named: OP2 within residue: .R<DT5 1>
Created a new atom named: OP3 within residue: .R<DT5 1>
Created a new atom named: N9 within residue: .R<DT 10>
Created a new atom named: N7 within residue: .R<DT 10>
Created a new atom named: C8 within residue: .R<DT 10>
Created a new atom named: N6 within residue: .R<DT 10>
First, your first residue has a terminal phosphate group, but standard
Amber libraries don't contain a 5' phopshate. Second, residue 10 claims to be
a thymidine, but the atom names don't match that of thymidine.
See section 3.2.3 of the Amber2017 Reference Manual for instructions on how
to handle the first problem (depends on whether you want the 5' phosphate
there or not). The solution to the second problem will depend on how you
created the pdb file, and on what is really intended to be at residue 10.
....dac
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Received on Sun Jul 30 2017 - 18:30:03 PDT
