On Mon, Dec 03, 2012, Thomas Evangelidis wrote:
>
> I want to create .prmtop and .inpcrd files for a protein/retro-inverso
> peptide complex. I've read in older posts that there is no need to modify
> any amber99sb (or its variants) library to include D-amino acids. However,
> when I use regular amino acid names for the D- amino acids in the pdb file
> I get errors like:
>
> FATAL: Atom .R<NASN 1>.A<HB1 19> does not have a type.
You don't say how you created your input pdb file, but it looks like it is
using the "old" (pdb version 2) atom names. I think you can get "reduce" to
update the names, or protonate can do it. If there are just a few D-amino
acids, you might even rename by hand.
>
> and warnings like:
>
> WARNING: There is a bond of 4.673348 angstroms between:
> ------- .R<NASN 1>.A<C 15> and .R<GLU 2>.A<N 1>
This is a pretty straightforward message: if you indeed have such a long
peptide bond in the PDB file, you need to address the question of how it got
there.
....dac
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Received on Sun Dec 02 2012 - 18:30:02 PST
