On 11/12/12 9:17 PM, Rajiv Gandhi wrote:
Could someone tell how can i modify the specific force field, for example
gromacs43a1, to build topology file for protein has iron that interact with
some ligands (cytochrome, hemoglobin...etc)? which file i should modify?
Heme parameters already exist in the Gromos force fields. There are some
missing bonded parameters, as I recall, but people have used them for
simulations, so I suspect the necessary information is somewhere in the
literature. For searching purposes, it's best to use the correct terminology -
there's no such thing as a "Gromacs force field." The one you reference is
Gromos96 43A1, which is a specific parameter set within the Gromos96 family of
force fields.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
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 [email protected].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
