On Tue, Oct 13, 2015, Hadeer ELHabashy wrote:
>
> I have a pdb file consists of four identical peptides and I want to
> simulate them together. However Amber can not detect many atoms with
> similar names or similar residue number. I have tried to change the atoms
> names or the residues names but xleap has many problem with this and some
> structure deformation happened . what exactly should I change to save the
> structures without xleap fatal errors .
Put a TER card in the PDB file after each of the chains (peptides).
...good luck....dac
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Received on Tue Oct 13 2015 - 18:30:03 PDT
