Tanos Franca wrote:
Dear GROMACS users,
We're trying to perform a MD simulation of a system with a hematin
group but realized that GROMACS does not have parameters for the ion
FE2+. We tried to include the parametrs in the file ions.itp but did not
suceed yet. Does anybody knows the right procedure to introduce this
It would be helpful to know exactly where you're stuck, otherwise we're left
guessing as to what you've tried.
ions into the file ions.itp ? Do we have to change anything more in
order to GROMACS recognize the new ion ?
You may have to introduce a new atom type into the .atp file, and set nonbonded
parameters for it in ffnonbonded.itp, but also be aware that a crude
representation of a transition metal as a normal point charge may not be
terribly accurate:
http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species
Also, please do not send messages that copy the entire digest (or any unrelated
content, for that matter). It confuses the archive.
-Justin
With my best regards,
Tanos C. C. Franca.
Coordinator of the Graduate Program in Chemistry
Military Institute 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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