[gmx-users] Re: how modify the forcefield amino acid definitions for non-naturally occuring amino acids?

Justin A. Lemkul jalemkul at vt.edu
Mon Mar 5 14:10:23 CET 2012

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 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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