From: thiagorrg UFC (thiagorrgarcia_at_alu.ufc.br)
Date: Wed May 02 2018 - 12:00:05 CDT
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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