[gmx-users] capping in c terminal

Mark Abraham Mark.Abraham at anu.edu.au
Sat Feb 21 11:41:44 CET 2009

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.


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