From: Isuru Herath (
Date: Sun Jan 10 2021 - 12:58:16 CST


I am following the "Residue-Based Coarse Graining using MARTINI Force Field
in NAMD" Tutorial and I am having trouble with the step that says to
correct the CG file to include the secondary structures. When I run ...

1. source fix_martini_psf.tcl
2. fix_martini_psf 0
01-CG-lipoprotein_autopsf.psf 01-CG-lipoprotein_autopsf.pdb
CG-fix_martini_psf 1 ../05-scripts 1 -1

The resulting CG-fix_martini_psf files are produced without any errors
showing up however, when I compare the CG-fix_martini_psf.psf file with the
original CG file pre-correction, the secondary structures have not changed.
Thus, backbone beads still have generic types like "P5" instead of "QDC" as
the given example output files do. If someone could provide help on this, I
would greatly appreciate it.

Thank you,