Hello all, I am using charmm ff in Gromacs 4.5.2, everything goes right with standard proteins, but now i want to run a simulation on a protein with a phosphorylated residue. As mentionned in this post http://www.mail-archive.com/gmx-users@gromacs.org/msg35532.html, I changed the rtp and hbd to add a specific section for the phosphorylated amino-acid, having checked the parametres with charmm. I still have the problem in pdb2gmx where it seems like he can't see the new definition and gives me the residue topology database error. Is there another file where I have to specify the new amino-acids, I search all the files in the charmm directory in gromacs top, but I still can't find another place where amino-acids are defined. Thanks for you help
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