Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Issues regarding scripts to run MD Simulation #114

Open
nilanjana1996 opened this issue Jun 19, 2024 · 1 comment
Open

Issues regarding scripts to run MD Simulation #114

nilanjana1996 opened this issue Jun 19, 2024 · 1 comment

Comments

@nilanjana1996
Copy link

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
Copy link

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

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants