Issue for backmapping from MARTINI3 to All-atom with backward-v5 / initram-v5.sh

[JingkaiZeng]

Hi,

I am trying to use the backward method as outlined in the tutorial on reverse coarse-graining with Martini 3 "https://cgmartini.nl/docs/tutorials/Martini3/Backward/#backmapping-from-martini-3". I am using a Python 2 environment to run initram-v5.sh, following the tutorial steps.

However, I encountered the following error:

(python2) [mdmm@n3 LPBE-test]$ ./initram-v5.sh -f step7_production.gro -o aa.gro -from martini -to charmm36 -p topol.top

initram.sh version 0.1:

(c)2013 Tsjerk A. Wassenaar, PhD

University of Calgary
2500 University Drive NW
Calgary, Alberta
Canada, T2N 1N4

Now executing...

./initram-v5.sh -f step7_production.gro -o aa.gro -from martini -to charmm36 -p topol.top

Checking dependencies:
backward.py ... /usr/bin/which: no backward.py in (/home/mdmm/miniconda3/envs/python2/bin:/home/mdmm/.local/bin:/home/mdmm/bin:/home/mdmm/cg2at:/usr/local/gromacs/bin:/usr/local/Modules/bin:/usr/local/anaconda3/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin)
~/LPBE-test/backward.py
gmx ... /usr/local/gromacs/bin/gmx
/home/mdmm/LPBE-test/backward.py -f step7_production.gro -raw projected.gro -o 0-backward.gro -kick 0.05 -sol -p topol.top -po backmapped.top -n backmapped.ndx -from martini -to charmm36
Error reading amber to martini mapping for GMO (file: /home/mdmm/LPBE-test/Mapping/nac.oplsaa.map).
Error reading amber94 to martini mapping for GMO (file: /home/mdmm/LPBE-test/Mapping/nac.oplsaa.map).
Error reading amber96 to martini mapping for GMO (file: /home/mdmm/LPBE-test/Mapping/nac.oplsaa.map).
Error reading amber99 to martini mapping for GMO (file: /home/mdmm/LPBE-test/Mapping/nac.oplsaa.map).
Error reading amber99sb to martini mapping for GMO (file: /home/mdmm/LPBE-test/Mapping/nac.oplsaa.map).
Error reading amber03 to martini mapping for GMO (file: /home/mdmm/LPBE-test/Mapping/nac.oplsaa.map).
Error reading amberGS to martini mapping for GMO (file: /home/mdmm/LPBE-test/Mapping/nac.oplsaa.map).
Traceback (most recent call last):
  File "/home/mdmm/LPBE-test/backward.py", line 644, in <module>
    struc = Structure(options["-f"].value,strict=options["-strict"].value)
  File "/home/mdmm/LPBE-test/backward.py", line 410, in __init__
    d12.append(d12[-1])
IndexError: list index out of range

My system consists of a protein-membrane (POPC) with an elastic network in Martini 3. Does anyone have suggestions on how to resolve this issue?

Thank you!