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3 years 6 days ago #8920 by fviscarra
Backmapping protein-membrane system built with insane was created by fviscarra
Hello

I built a protein membrane system using insane.py script, and I'm trying to backwards mapping it with initram-v5.sh, but I get the following error while running the script:

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 ../a6b2b3_membrane.gro -o ../atomistic.gro -to charmm36 -p ../a6b2b3_membrane.top

Checking dependencies:
backward.py ... /biggin/b196/scro4068/martini/backwards/backward.py
gmx ... /sbcb/packages/opt/Linux_x86_64/gromacs/2020_GCC6.2_CUDA10.1.AVX2/bin/gmx
/biggin/b196/scro4068/martini/backwards/backward.py -f ../a6b2b3_membrane.gro -raw projected.gro -o 0-backward.gro -kick 0.05 -sol -p ../a6b2b3_membrane.top -po backmapped.top -n backmapped.ndx -from martini -to charmm36
Traceback (most recent call last):
  File "/biggin/b196/scro4068/martini/backwards/backward.py", line 638, in <module>
    top = options["-p"] and Topology(options["-p"].value,out=options["-pp"].value)
  File "/biggin/b196/scro4068/martini/backwards/backward.py", line 543, in __init__
    self.atoms = [[a,r,i,c,0,0,0,t] for t,c in mr for a,r,i,m in self.moleculetypes[t]]
KeyError: 'protein'

It looks like the error is in the topology file, but that file was generated with the insane script so I don't really know what to do about it.

I would be thankful if anyone can help me.

Bests

Franco

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3 years 5 days ago #8921 by tsjerk
Replied by tsjerk on topic Backmapping protein-membrane system built with insane
Hi Franco,

For the topology, you need to provide an atomistic one, describing the system you want to map to.

Cheers,

Tsjerk

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