Tanos Franca wrote:
Dear Gromacs users,
I'm sure that the Gromos5A36 force field have topology to the heme
group and would like to know how to proceed to perform a successfull MD
simulation on a protein with this group. Should I just write the name of
the heme topology file inside the protein.top file (just like we do with
ions.itp) ? We also would like to confirm the name of the heme topology
file. Is it heme.rtp ?
No. The heme group is defined in aminoacids.rtp as HEME, and any special bonds
between the heme prosthetic group and amino acid sidechains is handled by
specbond.dat, thus the heme becomes part of the protein moleculetype.
That said, there have been plenty of posts to the list that there are errors
when running grompp (missing bond and angle parameters, usually) such that the
presence of heme groups may not work out of the box, so to speak. Of course,
plenty of heme simulations have been reported in the literature, so those bonded
parameters must exist somewhere.
-Justin
Thank you in advance.
Tanos C. C. Franca.
Coordinator of the Graduate Program in Chsmistry.
Military Intitute of Engineering.
Rio de Janeiro - RJ
Brazil.
--
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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