[gmx-users] file heme.rtp

Justin A. Lemkul jalemkul at vt.edu
Wed Jan 12 02:04:22 CET 2011

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.


>     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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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