I got it, thank you so much sir
On Wed, Jul 5, 2017 at 6:40 PM, David A Case <david.case.rutgers.edu> wrote:
> 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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--
*Regards,*
*Nadia Rahmah*
*Department of Physics Undergraduate Student - 2013Bogor Agricultural
University*
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Received on Thu Jul 06 2017 - 20:00:03 PDT
