[gmx-users] Phosphorylated Serine in charmm

Yasmine Chebaro yasmine.chebaro at gmail.com
Fri Nov 26 11:16:03 CET 2010

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
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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