Kirill Bessonov wrote:
Thank you Justin for your prompt reply, as usual :)
With the last 2 lines of my previous post, I was referring on how to
build *.itp files for completely new molecules (say lipids such as DMPC,
DMPE or glutathione) that are not defined in the forcefield. I.e. how to
derive dihedral angle code, force constant, etc. so that this new
molecules could be used in the simulation. I.e. how to build your own
*.itp and *.top files. Or better said, how the parameters for already
defined molecules in the forcefield, such as amino-acids and ions were
created? Where can we get more information about this ins and outs of
building your own topologies? Maybe there are some good references that
you can refer me?
Read the primary literature for whatever force field(s) you're interested in.
Parameterization methodology should be present in the original publications or
any that refer to modifications of the original parameter set. Details can be
sketchy depending on the force field, so be prepared to invest significant time
in this endeavor.
-Justin
--
========================================
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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