[gmx-users] Termini for a collection of fractions of protein in one pdb file

[Markus O Kaukonen]

Dear All,

I have a collection of pieces of protein in one pdb file
(obtained by taking all atoms closer than xx au from iron and
not breaking any amino acids.)

However, pdb2gmx only set correct termini (NH3+ or COO- in my case)
to aminoacids that are at the beginning and in the end of the pdb file,
and termini (of protein fractions) sitting in the middle of the
pdb file are lef untouched (which is incorrect).

Question: Has someone coded a program that puts different pieces of
protein in different pdb files or solved this problem by some other means?
(Did not find this in the manual or FAQ).
Or do I have to do it myself (breaking the protein by hand to various pdb
files is too much for me).

Terveisin, Markus



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