On Tue, Apr 07, 2015, Vaibhav Dixit wrote:
> I have prepared the PDB in Schrodinger package (attached) ....
> Loading PDB file: ./1W0E_prepared.pdb
> Created a new atom named: H within residue: .R<ACE 24>
This means that you have a residue named "H" in your pdb file, which is not in
the Amber residue (from its library) named ACE. Atom names in the PDB file
and in the residue libraries must match exactly. You will need to edit
your PDB file fix this. Same for the other "new atom" commands listed below:
> Created a new atom named: H1 within residue: .R<TYR 25>
> Created a new atom named: HE2 within residue: .R<GLU 97>
> Created a new atom named: HD2 within residue: .R<ASP 270>
> Created a new atom named: HE2 within residue: .R<GLU 320>
> Created a new atom named: HD1 within residue: .R<HIE 324>
> Created a new atom named: HD1 within residue: .R<HIE 402>
> Created a new atom named: H1 within residue: .R<CTHR 499>
> Created a new atom named: H2 within residue: .R<CTHR 499>
For the histidines, note that the default in Amber is for histidines to be of
type HIE. But your pdb file has hydrogens that make this either HID or HIP.
Also, it looks like the preparation scheme you used has neutral carboxylates
at residues 97, 270 and 320. You will have to decide if these are what you
want or not. Protonated residues in Amber are called ASH and GLH.
p.s.: We recommend that you use ff14SB, not ff99SB.
...dac
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Received on Tue Apr 07 2015 - 05:30:03 PDT
