r/comp_chem

Hello everyone, can you help me troubleshoot this error I keep on encountering while running a geometry optimization job? I've tried varying the number of processors from 2 to 8, running in serial calculation instead of parallel, tried removing the TightSCF parameter, even restarted my laptop a numerous times but the error still keep on persisting. I'm geometry optimizing a sole diethyl ether ligand where one of the H is substituted with F. I hope you can help me based on these output files, I've run out of ideas to try to mitigate this error.

https://drive.google.com/drive/folders/1I4TgeYnNz2ReQBmf94Q8Egv\_LzP76WSX

I work through Szabo Ostlund and on page 88 (2.3.7 Pseude-Classical Interpretation of Determinantal Energies) it says that "The exchange Interactions between electrons with parallel spin are not real physical interactions but a convenient way of representing the energy of a system described by a single determinant. The physical interaction between two electrons [...] does not depend on the spin of the electrons"
This is the part where they introduce the idea that the energy of a single determinant can be summed up with H, J and K Terms.

Now consider a single determinant with two spacial orbitals. Both are occupied with one electron each. In case 1), both electrons have the same spin. In case 2), both electrons have opposite spins.

From Chemical knowledge I know that 1) is singulet and 2) is triplet and energy wise the triplet state is lower in energy. This is measurable.

Now the theory with this "adding up H, J and K terms to get determinantal energies" also predicts the same as:

Energy of 1) = H11 + H22 + J12

Energy of 2) = H11 + H22 + J12 - K12

So the - K12 lowers the energy of the triplet state which we measured and therefore proved correct.

But on the other hand Szabo Ostlund says that this exchange interaction is not physical.

How can this be not physical if we can measure it and the theory correctly predicts the relative energies of those two determinants?

I recently worked on a small project as part of my course in QC Modelling which has me performing MD on a protein (Lysozyme and some others), and then running the results through an MSM( Markov State Model ) with pyemma and deeptime.

The results aren't really spectacular mainly because I didn't have access to a cluster then(and neither do I have it now), and my MD trajectories were too small for it.

I have been wanting to extend it into a full length project (by length I mean something that is more than popping an MD traj into a MSM tutorial I found online). Would anyone suggest any extensions to the project?

Would love to hear your thoughts and maybe any literature you'd recommend me to read up on?

Hi all,

I have a 16-aa cyclic peptide with a non-standard thioether linkage, and I generated thousands of 3D conformers with Rosetta SimpleCycPepPredict using -cyclic_peptide:cyclization_type thioether_lariat.

I’d like to dock these conformers in batch against a known protein-protein interface while keeping the thioether intact. Many docking tools, including some supporting cyclic peptides, either cannot handle the non-standard linker or require opening the cycle.

What docking tool or workflow would you recommend?

Thank you so much :)

Hi all,
I’m preparing a protein receptor for AutoDock Vina screening at pH 7.4.

PROPKA gives three potentially relevant His residues with predicted pKa values of 7.26, 7.35 and 8.07. They are currently modeled as neutral HID/HIE states.

Would you:

• protonate the pKa 8.07 His to HIP,
• keep the borderline ones neutral,
• or test multiple receptor protonation states for docking?

How much weight would you give to PROPKA versus local H-bond geometry / experimental structures when deciding?

Thanks!

Hey everyone! I’m currently an MSc student planning my thesis around computational drug discovery/CADD.

​I’m looking to connect with fellow students, beginners, or enthusiasts who want to motivate each other.

​If anyone is interested we can do chatting to bounce ideas around, feel free to drop a comment or send a DM!