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Backmapping protein-membrane system built with insane
- fviscarra
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3 years 2 weeks 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:
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
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 2 weeks 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
For the topology, you need to provide an atomistic one, describing the system you want to map to.
Cheers,
Tsjerk
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