On Mon, Sep 23, 2019, Shankha Banerjee wrote:
>I have been trying to run simulations (using Amber 18) for my protein
>containing a modified amino acid. The N-terminal has a myristic acid
>connected to Asp as a modification.
>Loading PDB file: ./try_out.pdb
>
>/home/suchetana/amber18/bin/teLeap: Warning!
>Name change in pdb file residue 1 ;
>this residue is split into MY and ASP.
>
>/home/suchetana/amber18/bin/teLeap: Note.
>1 residues had naming warnings.
>Thus, there are split residues;
>residue sequence numbers will not correspond to those in the pdb.
>-- residue 1: duplicate [ cD] atoms (total 13)
Your input pdb file looks like it has serious problem: atom names within
residue names are not unique -- this is not allowed in Amber.
>
>Atom names in each residue should be unique.
> (Same-name atoms are handled by using the first
> occurrence and by ignoring the rest.
> Frequently duplicate atom names stem from alternate
> conformations in the PDB file.)
>
>Created a new atom named: cC within residue: .R<MY 1>
>Created a new atom named: oC within residue: .R<MY 1>
>Created a new atom named: cD within residue: .R<MY 1>
These three atoms are present in the PDB file, but not in the
"MY" residue unit.
> Added missing heavy atom: .R<MY 1>.A<C12 38>
> Added missing heavy atom: .R<MY 1>.A<C13 35>
> Added missing heavy atom: .R<MY 1>.A<C14 32>
> Added missing heavy atom: .R<MY 1>.A<C15 29>
> Added missing heavy atom: .R<MY 1>.A<C16 26>
> Added missing heavy atom: .R<MY 1>.A<C17 23>
> Added missing heavy atom: .R<MY 1>.A<C18 20>
> Added missing heavy atom: .R<MY 1>.A<C19 17>
> Added missing heavy atom: .R<MY 1>.A<C110 14>
> Added missing heavy atom: .R<MY 1>.A<C111 11>
> Added missing heavy atom: .R<MY 1>.A<C112 8>
> Added missing heavy atom: .R<MY 1>.A<C113 5>
> Added missing heavy atom: .R<MY 1>.A<C114 2>
The above atoms are present in the MY residue unit (library), but are
not present in the input PDB file.
Basically: the atoms and residues in the PDB file have to exactly match
the atom and residue names in the amino acid libararies you are using.
....hope this helps....dac
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Received on Mon Sep 23 2019 - 09:00:02 PDT
