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Hello Daniel--

> 
> Problem solved. The numbering of the residues was shifted.
> Strangely that doesnt give you an error in the process but messes up
> the terminus. 

Perhaps this is the problem: if you add an ACE to the beginning of the
sequence using seq2psf, by default, the residue numbers of the other
residues are incremented by one. This can be avoided by providing the
- -startresid option to seq2psf. e.g.

  seq2psf -startresid 0 aceadded.seq > new.psf

best regards--
Charles
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