Hello,
I have really enjoyed using your incredibly comprehensive and user-friendly program. I cannot overstate how much I appreciate it. I'm encountering a discrepancy though that I can't explain. It probably shows a lack of basic understanding on my part, but
I would be grateful if you could help me figure this out.
I have not been able to find 3D structure files for all of the ligands I'd like to run, so I have been using Chimera to build structures from the canonical SMILES presented on PubChem. I have also been using Chimera to minimize these structures. In order
to be sure that the structures are completely minimized I've used the following...
|
Steepest descent steps |
1000 |
| Steepest descent step size |
0.02 |
| Conjugate gradient steps |
10000 |
| Conjugate gradient step size |
0.002 |
I ran this minimization and then AutoDock Vina for both the SDF and SMILES-built versions of several ligands. Both versions came from the same page (I was using PubChem) and both versions seemed to get minimized completely (the minimization outputs ended with
many rows of RMSDs of zero). I'm confused that I'm getting different energy values (both initial and after minimization) for the two versions and I'm getting slightly different docking results as well.
- Is it expected that SMILES and SDF files of the same chemical should have different energy values even after minimization?
- Would you recommend using Zinc (aromatic) SMILES to build structures instead of the canonical smiles on PubChem? OR would you recommend using PubChem CIDs instead of SMILES?
Thank you so much in advance for your time and guidance.
Best regards,
Kelly Kerr