On 20/09/2012 1:08 PM, Rajiv Gandhi wrote:
Dear all,

Why all people cut the protein ligand bond to produce the photodissociation?

Because MM forcefields typically assume bonds do not break or form. Electronic degrees of freedom are not directly considered in the model.

For instances, In myoglobin, To simulate photodissociation of the CO
complex, the Fe–CO bond of the
starting structure was cut before any calculation.Fe-C bond were cut and
instantaneously switch the heme force
field from 6-coordinated Fe to that of the 5-coordinated Fe.



I want to understand how we can delete this bond between Fe-CO  to induce
the photodisssociation ?  After we cut the bond what it can do during MD
simulation ?

If you know enough about such a system to parametrize the bonded and non-bonded systems, then in principle you could watch the process of dissociation after cleavage. But I can imagine spending 6 months to do that parameterization and still failing. A modelling approach that works nicely for simple first- and second-row elements not undergoing chemical reactions need not be extensible to either transition elements or reactions.

Mark
--
gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Reply via email to