[gmx-users] MD simulation of peptide amphiphile using CG method

[Graham J.A.]

You can take the standard parameters for the amino acid and hydrocarbon
components, but as you said, the difficulty is in the link.  You'll need
to find an existing MARTINI molecule with a similar link in it and take
the parameters from that.  If there isn't an existing molecule you can
copy from then the easiest way to get the new parameters is from
atomistic simulation.

It's also important to validate any new CG model which can be done
either against experimental data, or again against atomistic simulation
(ideally both).

Martinize.py will only be able to convert an atomistic structure if the
molecule has been defined in its database, it won't work on a new
molecule until you tell it the parameters to use.  It's obviously
recognising the protein component and giving you parameters for that,
but doesn't know what to do about the hydrocarbon tail.

Yes, the easiest thing to do would be to copy a residue from the amino
acids itp and modify it there, but you'll still need to get the
parameters of the bond to the hydrocarbon tail.

James


On Fri, 2017-02-03 at 18:53 +0330, leila karami wrote:
> Dear James,
> 
> Thanks for your answer.
> 
> As I understand, PyCGTOOL generates the coarse-grained molecular dynamics
> models from atomistic simulation trajectories. But, I don't want to do
> the atomistic simulation.
> 
> Also, ATB only generates a complete topology for molecules containing < 40
> atoms, while I have 5 PA molecules with > 40 atoms, apiece.
> 
> Since my molecules contain amino acids bonded to the hydrocarbon chain
> (which are default beads in Martini force field), I think there is
> a straightforward way for treatment of that. Unfortunately, I don't have
> experience about that. My problem is how to relate amino acids to hydrocarbon
> chain?
> 
> When I use martinize.py, in structure and topology output files, there are
> only amino acids and not hydrocarbon chain.
> 
> Should I modify martini_v2.2_aminoacids.itp by adding hydrocarbon tail
> parameter to it?
> 
> Best,
> LK