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pablo-arantes / making-it-rain

Cloud-based molecular simulations for everyone
MIT License
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Issues regarding scripts to run MD Simulation #114

Open nilanjana1996 opened 3 months ago

nilanjana1996 commented 3 months ago

I was trying to use the Google colab based Notebook "Making it Rain" to perform molecular dynamics simulation of one of my proteins with the small molecule inhibitor. But I am getting issues in te following line. I was wondering if you could help me with this.

!grep "Volume:" leap.log > temp.txt with open("temp.txt", 'r') as f: for line in f: vol = float(line.split()[1])

*vol_lit = vol pow(10, -27)* atom_lit = 9.03 pow(10, 22) conc = float(Concentration) num_ion = int(vol_lit (conc/0.15) atom_lit)

if Ions == "NaCl": pos_neut = "Na+ 0" pos_num = "Na+ " + str(num_ion) Cl_num = num_ion else: pos_neut = "K+ 0" pos_num = "K+ " + str(num_ion) Cl_num = num_ion

I would be grateful if you kindly let me know how to get past this issue. Thank you. The screenshots are attached for your referecne.

Thank you Best regards Screenshot 2024-06-19 180156 Screenshot 2024-06-19 180209

noumanistic commented 3 months ago

Sir did you found any solution to this problem? I am facing the same issue.

havid97 commented 1 month ago

i am facing the same issue