On Thu, Jun 10, 2010, Andrew Voronkov wrote:
> PS GLU is terminal, this is dimer, in each case this GLU ressidue is N
> terminal, but maybe I need to add manually NGLU, but agains it's strange
> why ambpdb doesn't do it in a way that leap can read then and save
> parameters.
I think everyone on the list is completely guessing here -- have you posted
a complete example that fails? You say "a file that was generated by amber",
but we don't know how it was generated, nor how it was used.
Much grief (but eventually much good as well) was caused by the fact that
the PDB recently changed its atom names, especially for hydrogens, but also
for some heavy atoms. Amber has tried to keep up with the change, and to the
extent possible, still deal with older files.
If you have two separate amino acid strands, be sure there is a "TER" card
separating them in PDB files that you load into LEaP.
....dac
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Received on Thu Jun 10 2010 - 18:30:05 PDT
