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.
-Justin
Thanks for you help
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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