Hello Yi--
>
> I am attempting to add an unstructured peptide (about 40 residues) after the
> N-domain of a protein. This C-terminus is not presented in the pdb file.
> There is no restraint between the N-domain and the C-terminus. I also want to
> perform a minimization which fix the N-domain and allow the C-terminus to
> sample the space. Can I use the ?patch? command and how?
>
To generate a complete pdb you can follow the example in
eginput/PSF_generation/addAtoms2.py
With this procedure, you specify the sequence of the full protein and
then load the known coordinates. An explicit patch statement is not
necessary.
Do let me know if you have further questions.
best regards--
Charles
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--
Charles Schwieters email: Charles at Schwieters.org
www: http://schwieters.org/cds
phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt
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