Comments (3)
I don't see where in the code this would be happening. Can you try the latest version (1.2.0) and if it doesn't work send me the input and output?
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Hi @Tsjerk .
I am experiencing the same issue with the pip installable version.
Did you get a chance to look at the files?
Otherwise, I can provide the files to reproduce this issue.
Best,
Amin.
from insane.
Hi @aminsagar,
I haven't done any CG simulations in a long time, but i stumbled over this publication: https://pubs.acs.org/doi/10.1021/acs.jctc.3c01222. Under associated content they have a link to a tutorial for switching Go̅ -Martini simulations. And in this tutorial they describe the same problem with a quite elegant solution. I will add the tutorial.
Here a snippet of the tutorial and the full tutorial:
wget http://www.cgmartini.nl/images/tools/insane/insane.py
python2 insane.py -f Protein_Active_cg.pdb -box 8,8,10 -l POPC -o ions.gro
-salt 0.15 -charge auto -center -sol W
2>system.top
Repair the wrong ion names and ion counts.
sed -i "s/NA+
NA+/NA
NA/g" ions.gro
sed -i "s/CL-
CL-/CL
CL/g" ions.gro
sed -i "s/NA+/NA /g" system.top
sed -i "s/CL-/CL /g" system.top
vi system.top # Delete 2 CL in system.top and ions.gro. The error is becaus
e the virtual atoms without charges are also calculated by insane.py.
vi ions.gro
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