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

Kirill Bessonov kbessonov at gmail.com
Mon Mar 5 05:33:03 CET 2012

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?
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