On Tue, 2014-04-08 at 11:28 +0530, Arunima Shilpi wrote:
> Dear Sir
>
>
> Presently I am studying protein-ligand interaction in which one of the
> residue along the active site have been mutated to ILE . Now when I load
> the protein in tleap it shows the following error
>
> complex=loadpdb C1191I_ZINC7271_min.pdb
> Loading PDB file: ./C1191I_ZINC7271_min.pdb
> Created a new atom named: CD within residue: .R<ILE 709>
> Added missing heavy atom: .R<ILE 709>.A<CD1 14>
> Created a new atom named: CD within residue: .R<ILE 731>
> Added missing heavy atom: .R<ILE 731>.A<CD1 14>
> Created a new atom named: CD within residue: .R<ILE 752>
> Added missing heavy atom: .R<ILE 752>.A<CD1 14>
All of your isoleucine residues have an atom named 'CD' in them in your
PDB file. The way tleap works is it matches the residues in your input
structure to the residue libraries that have been loaded before. That
is how it knows what connectivity and atom types to assign to all of the
atoms in each of the residues. A caveat of that approach is that all of
the atom names in your input structure must match _exactly_ the atom
names of the corresponding atoms in the LEaP library files. Any atom
that is _not_ in the input structure but is in the library file is
automatically added by LEaP.
This message states that a new atom was added to the residue (CD) which
was not in the template. Right after that, it says that LEaP adds a
missing atom CD1. This happens because the ILE residue in the Amber
library files name the delta-carbon in isoleucine CD1, but your PDB has
it named CD. If you change the names of CD to CD1 in your input PDB
file, this error will go away.
As a side-note, the atom names in Amber's library files are set to the
names used by the latest version of the PDB standard. So any PDB you
download today should work with the existing names (unless of course you
have a non-standard residue that has not yet been parametrized).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Apr 08 2014 - 05:00:03 PDT
