normal Problem using initram / backward

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4 years 7 months ago #8230 by jf009
Problem using initram / backward was created by jf009
hello how r u
i am trying to use initram.sh but i keep getting this error

./initram.sh -f CG.gro -p system.top -to gromos

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.sh -f CG.gro -p system.top -to gromos

Checking dependencies:
backward.py ... /Users/jf/backmap/backward.py
grompp ... /usr/local/gromacs/bin/grompp
mdrun ... /usr/local/gromacs/bin/mdrun
/Users/jf/backmap/backward.py -f CG.gro -raw projected.gro -o 0-backward.gro -kick 0.05 -sol -p system.top -po backmapped.top -n backmapped.ndx -from martini -to gromos
Error reading amber to martini mapping for GMO (file: /Users/jf/backmap/Mapping/chol.amber.map).
Error reading amber94 to martini mapping for GMO (file: /Users/jf/backmap/Mapping/chol.amber.map).
Error reading amber96 to martini mapping for GMO (file: /Users/jf/backmap/Mapping/chol.amber.map).
Error reading amber99 to martini mapping for GMO (file: /Users/jf/backmap/Mapping/chol.amber.map).
Error reading amber99sb to martini mapping for GMO (file: /Users/jf/backmap/Mapping/chol.amber.map).
Error reading amber03 to martini mapping for GMO (file: /Users/jf/backmap/Mapping/chol.amber.map).
Error reading amberGS to martini mapping for GMO (file: /Users/jf/backmap/Mapping/chol.amber.map).
Traceback (most recent call last):
File "/Users/jf/backmap/backward.py", line 645, in <module>
top = options["-p"] and Topology(options["-p"].value,out=options["-pp"].value)
File "/Users/jf/backmap/backward.py", line 550, 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: 'POPC'

i am trying to convert it from martini to gromos. why does this happen and can it be fixed?

thank you for your help =)

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4 years 6 months ago #8238 by riccardo
Replied by riccardo on topic Problem using initram / backward
Are you using the latest version of backward available from github.com/Tsjerk/Backward ? If not, I would recommend to switch to that.

Not sure what the "Error reading amber to martini mapping for GMO " are about but your error seem to have to do with POPC. You have POPC in the system I would guess? Are the CG.gro and system.top files in agreement - e.g., you have 20 POPC followed 300 W both in the .gro and .top files?

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