shahrbanoo karbalaee wrote:
Dear justin
Hi,
about NH2 in c terminal peptide,do we need to chang rtp file for last
aminoacid,although there is NH2 in that and define it?or is it
enought to have pdb file and choose none option for c termial?
Each different residue in your structure file needs to map to a
correctly-formed .rtp file entry. If you wish to use pdb2gmx to modify
the termini, then the structure file, the .tdb and .rtp files need to be
self-consistent. If you want to have some non-amino-acid fragment (like
NH2) as your C-terminal group, then you will need to make sure the above
is true. There are various ways of doing this.
Mark
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