Re: Martini CG parameter errors for lipids

From: Hyun (biophysics1_at_gmail.com)
Date: Sun May 06 2018 - 08:52:44 CDT

Thiago

I don't know how CHARMM-GUI generate the parameters of coarse-grained
atoms, but you can check and use the parameter of NH3 from the tutorial
files if they use the same definition for NH3.

http://www.ks.uiuc.edu/Training/Tutorials/martini/
http://www.ks.uiuc.edu/Training/Tutorials/martini/rbcg-tutorial.pdf
(Appendix explainns NH3 in POPC)

Else, you can contact with CHAMM-GUI why you got an error.

Hyun

On Wed, May 2, 2018 at 12:00 PM, thiagorrg UFC <thiagorrgarcia_at_alu.ufc.br>
wrote:

> Hello everyone!
>
> It is my first time trying to simulate a CG system. I generated a lipid
> membrane (POPC/POPE/CHOL) using Martini Maker in CHARMM-GUI and i'm getting
> this error while trying to simulate:
>
> FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE NH3
>
> NH3 is the first atom in the POPE lipid. I know this error happens when
> the parameter file is not linked in the .conf file. I linked all of the
> martini parameters for CG available in the tutorial for NAMD and in the
> toppar available from CHARMM-GUI as below:
>
> # Input
> paraTypeCharmm on
> parameters ./toppar/martini-water.top
> parameters ./toppar/martini-ions.top
> parameters ./toppar/martini-protein-bonds.par
> parameters ./toppar/martini-protein-angles-cos.par
> parameters ./toppar/martini-protein-dihedrals.par
> parameters ./toppar/martini-all-nonb.par
> parameters ./toppar/martini-lipids-bonds-angles-dihedrals.par
> parameters ./toppar/martini_v2.2.namd.prm
> parameters ./toppar/martini_v2.2_aminoacids.auto.namd.cons.prm
>
> I'm sorry if this is a silly question, but i can't get past it. I don't
> know how to find the correct parameters file. Many thanks to everyone!
>
> --
> Thiago Garcia
>
>

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