How to enter a specific Ligand_isomer to generate a topology file

[Ash1000]

Hello, I have a basic question, my ligand generates four isomers. If I am not mistaken, I need to select one of them to generate topology. What character should I mention to pass the step and generate ligand_GAFF.pdb? Thanks

[pablo-arantes]

Hi,

You just need to type the number of your isomer. For example, if you want to select the isomer number 4, Ligand_isomer = 4. Follow the print:

I hope it helps.

Thank you.

Best,

Pablo

[Ash1000]

Thanks, Pablo, I have tried inserting numbers but every time it failed to generate the ligand_gaff.pdb. cat: /content/drive/MyDrive/1-Mcom/ligand_gaff.pdb: No such file or directory

NameError Traceback (most recent call last) in () 157 vol = float(line.split()[1]) 158 --> 159 vol_lit = vol pow(10, -27) 160 atom_lit = 9.03 pow(10, 22) 161 conc = float(Concentration)

NameError: name 'vol' is not defined