[gmx-users] Phosphorylated Serine in charmm

Justin A. Lemkul jalemkul at vt.edu
Sat Nov 27 04:46:51 CET 2010

Yasmine Chebaro wrote:
> 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.

The exact error message and what you have added to the .rtp and .hdb files would 
be very helpful (read: necessary) to give any useful advice.

> 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.

You will need to add your residue to residuetypes.dat as well.


> Thanks for you help


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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