On Wed, Jul 05, 2017, NADIA RAHMAH wrote:
> In tleap script, I have write savedpb, and it built a new pdb. When I open
> this pdb file, it still contain residue number 291 which is Alanin (residue
> number protein) and 292 is my ligand UNL. But, in leap log file, it written
> :
>
> Added missing heavy atom: .R<CALA 296>.A<OXT 11>
> Added missing heavy atom: .R<UNL 297>.A<C1 2>
> Added missing heavy atom: .R<UNL 297>.A<C2 4>
> Added missing heavy atom: .R<UNL 297>.A<C3 5>
> This is in complex pdb file:
I think we need to see the full "complex.pdb" file and the exact commands you
gave to tleap. The short description you gave above is indeed very odd: tleap
recognizes the ALA residue as a C-terminal one ("CALA") but doesn't like the
OXT atom in it. Something else is going on, either in the residue libraries
you loaded, or in the full contents of the pdb file, or in other tleap
commands that were executed. The bottom line is that just providing part of
the story is (in this case) not going to be enough.
Before sending additional information, look carefully at the "complex.pdb"
file for anything that might be odd in it. Make a simple tleap script (don't
try to handle more than one input pdb file, for example.) Try removing the
ligand, and just loading the protein part of the file. These tests may
help identify what is going on.
....dac
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Received on Wed Jul 05 2017 - 05:00:02 PDT
