Hi all,

I am an aspiring com chemist and I have recently endeavoured to try going through the TeachOpenCADD course materials by the Volkamer lab. Part of the requirements involve the use of smina to undergo docking studies.

However I am struggling to install smina. It doesn't appear to be available via condaforge. Navigating to the anaconda website and it doesn't appear that there is a version for macosx arm64, only osx64 the intel version. Attempting to compile from source code fails due to namespace errors between boost and std. I posted about this on the smina sourceforge forum if any one is interested (https://sourceforge.net/p/smina/discussion/help/thread/6b4d5f8d63/)

I am unsure if this is due to the fact that smina is incompatible with some new version of these 2 libraries, as the version requirements are not listed, or if smina simply isn't compatible with the arm64 architecture.

Hence I post here to ask if any of you have successfully installed smina on the arm64 architecture so as to avoid wasting any more time on this if it simply isn't feasible.

EDIT; Nvm, Im an idiot. Turns out the precompiled binaries were available through the downloads section of sourceforge the whole time.

So trying to replicate some data, They did an opt at low level, then did LC-wBPE after and they optimally tuned w to a value. In the SI they briefly explained that they used a did a golden section search to find the optimal value for w from some SPE calcs. I’m curious if anyone knows how this is actually done in practice. Is there a script that does it out there? What am I missing. Thanks

This post is for brainstorming. So please feel free to criticize!

I’m in the defense stage of my PhD in comp chem. I have worked over 5 years with different MD simulation packages and QM software programs and different types of chemical and biochemical systems. All in all to say I’m confident that I can work around any given problem without much problem.

So, I have been applying to postdoctoral position in computational biology/bioinformatics because that seems to be what the industry is going for and I wanted to expose myself to the tools and techniques.

My question is how easy is it to transition between these fields?

Am I wasting time here?

I think I am limited by options in my field since I’m constrained to a region due to family.

I haven’t seen any new ads for MD or molecular modeling expertise unless they require over 10+ years of experience.

What do you think?

Hello everyone,
I'm trying to simulate the adsorption of a N2 molecule on a Na(100) slab using QE. For the input I'm using a 12-layers Na 2 x 2 supercell with a 15A of vacuum keeping fixed the interlayers and letting free the 3 surface layers for both ends, with a N2 molecule in each surface oriented perpendicular to the surface.
Also i'm using:
- VdW correction DFT-D3
- assume_isolated=2D to truncate z-axis interaction
- nspin=2 for an unconstrained polarization

The calculation is not yet converged but it is going towards a shortenin of the N-N bond, opposite to what I would expect (ie. an elongation of the bond).
Am I doing something wrong that I can't see?

Thank you for your suggestions!

This is the main part of the input:

&SYSTEM
  ibrav = 0
  A =    8.30638
  nat = 52
  ntyp = 2
  ecutrho = 385 ! *11
  ecutwfc = 35
  occupations = 'smearing'
  smearing = 'gaussian'
  degauss =   0.01
  assume_isolated = '2D' ! annulla interazioni lungo asse z
  vdw_corr = 'dft-d3'  ! correzione per interazioni VdW
  nspin = 2
  starting_magnetization(1)= 0 ! Na
  starting_magnetization(2)= 0.1! N 
/

&ELECTRONS
  conv_thr =   1.0000000000d-6   ! Default 
  electron_maxstep = 400
  mixing_beta =   4.0000000000d-01
/

&IONS
  ion_dynamics = 'bfgs'
/
  
CELL_PARAMETERS {alat}
  1.000000000000000   0.000000000000000   0.000000000000000 
  0.000000000000000   1.000000000000000   0.000000000000000 
  0.000000000000000   0.000000000000000   4.683585508970213 
ATOMIC_SPECIES
  Na   22.98900  Na.paw.z_9.ld1.psl.v1.0.0-low.upf
   N   14.00650   N.oncvpsp.upf

Hello friends help me understand this terms and how it influence a small molecule.
i recently did a DFT calculation for rifampycin an inhibitor used as a first line therapy for mycobacterium tuberculosis. i wanted to conclude these datas into a meaningfull results.

Energy gap (aka.) HOMO LUMO gap

𝐸𝑔 = 𝐸𝐻𝑂𝑀𝑂 − 𝐸𝐿𝑈𝑀𝑂

Energy gap describes the reactivity of the molecule. smaller energy gap results in less stable compounds with greater reactivity, whereas a bigger energy gap corresponds to more stable compounds with reduced reactivity.  

Hardness  

𝜂 =𝐸𝐿𝑈𝑀𝑂 − 𝐸𝐻𝑂𝑀𝑂/2

what does hardness defines about ?

Softness 

𝜎 = 1/2𝜂

what does softness defines about ?

Chemical potential 

𝜇= 𝐸𝐻𝑜𝑚𝑜 + 𝐸𝐿𝑢𝑚𝑜/2

what does chemical potential defines about ?

electrophilicity index (ω)

 𝜔 = 𝜇^2/2𝜂

what does electrophilicity index defines about ?

Stabilization energy (Δ⁢E) 

Δ𝐸 = −𝜇^2/2𝜂

what does Stabilization energy defines about ?

Please help me.

I don't know how to apply it in practice to calculate the limit energy of the Complete Basis Set (CBS) using Gaussian16 software. I already have the geometry of the substances optimized at the MP2/aug-cc-pVTZ level of theory. What should I do next?

I am working on determing the mechanistic pathway for a hydosiliation reaction using Sn-based catalyst. I have optimized individually both reactants and products for the first step of the reaction using b3lyp/gen (6-311+g(d,p) for C, H, O, N and Si; and Lanl2dz (for Sn)). But I am facing issues with the appropriate ts search. Like the first step involves incoming of a benzaldehyde moiety in proximity of the catalyst. So I tried to perform both QST2, and QST3, where for the first frame I placed the two reactants a bit away from each other, in the second frame I simply placed the optimized structure of the entire assembly (i.e., the configuration where both the reactants are close to each, as obtained from a normal structure optimization). This I did for QST2. For QST3, I added another frame wherein the two molecules are in the middle way between reactants and products in terms of the distance between them.
The problem is the obtained ts vibration (corresponding to the imaginary frequence) is not representing the movement of the two molecules, rather it is just for a domain wise rotation. Also the corresponding imaginary frequency is very low, about -11. What else can I do here? Am I following a wrong approach here? Any help will do...Thank you in advance.

P.S I am using Gaussian 16, along with GaussView 6 for modelling and calculations.

Hi guys, may I ask how is vibrational analysis used to validate a benzene structure?

I asked my professor how to validate whether my optimised benzene structure on gaussian is accurate after running an opt_freq, and he told me to use vibrational analysis to predict frequency of vibrational modes. I don't get how that is used to validate my optimised structure.

If I were to get any explanation on this I am really thankful as my professor is not replying.

I am trying to get the UV-Vis spectra from a TDDFT calculation in VASP. I am following the instructions provided by the wiki(https://www.vasp.at/wiki/index.php/Time-dependent_density-functional_theory_calculations). It claims that the dielectric information should be present in the vasprun.xml file, but I cannot seem to find the information after running the second calculation specifying AGLO=TDHF with LOPTICS=.FALSE.

Does anyone know where the dielectric information should be printed after a TDDFT run?

Thanks.

I've prepared 17 proteins for binding site alignment however it gives this ERROR ref_list and mob_list must be the same length! I am really new to this program and I don't understand the problem I've tried it on two computers cuz the teacher told me that my comp might be the problem but still, this doesn't work

btw quick align works but teach doesn't like it for the reasons that I don't know so I need to do it

I have ran opt and freq calculations for a cation structure and have both alpha and beta eigenvalues. I am quite confused as to what the origin of these values are and which values to use to calculate the HOMO-LUMO gap. Apologies if this is very basic - I would be grateful if somebody could point me to resources or knows the answer as I am finding my searches not very clear.

I'm trying to run autodE by the Duarte group on an ubuntu machine with XTB and ORCA 6. I'm testing with their example of Diels-Alder.

It does start up but the really weird part is that ORCA just gets stuck somehow? sometimes I have orca_guess_mpi processes running that do nothing, sometimes it's orca_util_mpi, sometimes startup, sometimes the gradient, but it kinda just stops. If I take the input file autodE created and just run it using ORCA it works and is done in seconds.

This behavior makes absolutely no sense and I don't even know where to begin troubleshooting this.

So somehow autodE must be doing something differently and

Hi everyone,

I’m setting up an MD simulation in AMBER for Human Carbonic Anhydrase II (hCA II, PDB : 3KS3) with CO₂ and HCO₃⁻ (bicarbonate) as ligands. I have the PDB files for the protein, CO₂, and HCO₃⁻, as well as topology files for the ligands generated via ANTECHAMBER. I’m familiar with basic MD simulations (I’ve done some with hCA II in its apo form), but I’m seeking advice on integrating these ligands accurately.

Background on Mechanism:
hCA II catalyzes the reversible hydration of CO₂ to HCO₃⁻ and a proton. CO₂ binds in the active site’s hydrophobic pocket, located about 3.5 Å from the zinc ion. The zinc ion, along with residues His-94, His-119, Val-121, Val-143, Leu-198, and Thr-199, stabilizes the binding and promotes the conversion to bicarbonate through a zinc-bound hydroxide.

My Setup and Question:
Could anyone provide guidance or best practices for setting up the system in AMBER to ensure accurate ligand binding at these sites and thus setup my system for the given simulation? Any advice on constraints, positioning, or relevant commands would be greatly appreciated!

Thank you in advance!

Hi everyone! I want to run metadynamics simulations using Plumed patched with Amber. I know Amber is not so popular to use with Plumed, but somehow I have no choice other than this.

In the private cluster I am using, I am not been able to use GPU for it. For example, sander.MPI i.e. CPU works but pmemd.cuda doesn't. How do I enable and run my simulations in GPU for amber? Since , I am using CPU, the speed is very slow, sometimes like for a 5 ns run it takes ~30 hours which is not feasible at this moment.

My plumed version is 2.8

I am moderately new to comp chem and handling hpc environments. As I don't know what more information is needed to resolve this, feel free to ask for any clarification, any system configuration or any other requirement.

TIA

Asking here since I could find basically nothing like a tutorial or example online.

I've installed pre-complied xtb on my (windows) computer. But if I try to enter any of the commands I'm supposed to use xtb with in command prompt I just get 'xtb is not recognized', even when I do a cd command to move command prompt to the xtb file location. I don't have a computer science background. If someone could explain to me like I'm an idiot (which I may be) how I'm actually supposed to use xtb I'd appreciate it.

Hi

Has anyone any suggestions for getting a job related to the field, where to look, the best approach etc.. I am open to both academia and industry. My thesis focused mainly on DFT and Kinetic Monte Carlo.

Can anyone help or share their experience, please?

I'm having a problem with dipole correction using vasp.

Here's my INCAR:

----------------------------------------------------------------------------------------------------------------------------------------

global Parameters

SYSTEM = "12"

ISTART = 0 (Read existing wavefunction, if there)

LREAL = Auto (Projection operators: automatic)

ENCUT = 450 (Cut-off energy for plane wave basis set, in eV)

PREC = Accurate (Precision level: Normal or Accurate, set Accurate when perform structure lattice relaxation calculation)

NPAR = 10

LWAVE = .FALSE.

Electronic Relaxation

ISMEAR = 0 (Gaussian smearing, metals:1)

SIGMA = 0.01 (Smearing value in eV, metals:0.2)

NELM = 60 (Max electronic SCF steps)

NELMIN = 4 (Min electronic SCF steps)

EDIFF = 1E-06 (SCF energy convergence, in eV)

GGA = PE (PBEsol exchange-correlation)

Ionic Relaxation

NSW = 0 (Max ionic steps)

IBRION = -1 (Algorithm: 0-MD, 1-Quasi-New, 2-CG)

ISIF = 2 (Stress/relaxation: 2-Ions, 3-Shape/Ions/V, 4-Shape/Ions)

ISPIN = 2

LORBIT = 11

MAGMOM = 26*0 1 -1 -1 1

special:

LVHAR = .TRUE.

IDIPOL= 3

LDIPOL= .TRUE.

EPSILON = 1.00000

DIPOL = 0.5 0.5 0.5

EFIELD = 1e-12

-----------------------------------------------------------------------------------------------------------------------------------------------

I can't see the dipole correction, that is, the graph generated is not typical of this Vasp task.

Hi all,

I am very new to the comp chem world and want to do transition path sampling. I've tried finding guides online or examples of how to use different packages to do it but was not successful. I need QM support as I have bond breaks in my reaction path. An recommendations for packages to use (preferably in python) and guides or examples to follow?

Thanks,

David

I have a highly branched polymer (a type of polyglycerol) of about 300 atoms that I'm trying to run MD simulations on in openmm. I've drawn the molecule in avogadro, but since it isn't a protein the pdb file is just a bunch of atoms with UNK residue type, and all the force fields I've been able to find either want assume that you're working with a biological molecule with residue types for everything, and straight up don't work with my molecule. The stuff I've seen for force fields with arbitrary molecules assume the molecule to be very small, so those haven't too helpful either. Any advice on what I should try?

Hi everyone I’m early(ish) prof just tenured and I feel lost. My early career went really well, lots of great papers, students did well everyone was excited. Did a lot of work on clusters, moiety drug design etc. however my last great grad student just graduated this past summer and things have sort of taken a bit of a dive. Current crop of post docs have not been helping the younger students, and haven’t been as productive as I hoped. What’s worse is that I am sort of at a loss of where to go from here. Our major projects have all ended and nothing has spurred off from them as usual. I am in a funk and can’t come up with any project ideas that seem interesting. My one idea is too broad and I have no idea how to approach it. My students are all masters students and post docs at the moment and they all want things that can be done quickly. Seriously not sure how to go about getting this thing back in gear.

Hello all! I graduated this May with a Chemistry B.S. and a minor in computer informatics, and am currently working in a software development type role at a large tech company.

What I really want to do is computationally-aided drug design, and am currently applying to a couple PhD programs (ideally in CA for family reasons) this cycle, and likely applying to several more next cycle. I am not terribly interested in pchem or theoretical chem, but I simply love chemistry and programming, and the crazy developments these last few years in computation chem and bio are awe inspiring and I want to be a part of it. I am wondering if anyone has any recommendations for labs and PI's in California doing comp chem for drug design!

Also, I took a grad level spectroscopy class my senior year and was taken by surprise by how much I liked it, so If anyone knows of any labs in CA working on computational analysis of spectra I would be intrigued!

Hi! So this is honestly still a question for the future.
If everything goes to plan I'm going to get my master's in pharmaceutical engineering. At the beginning of my BSc I started a small research with one of my professors who is a computational chemist and I started to really like it to the point where my goal would be to do some computational work at a pharmaceutical company once I finish my degree. I started to consider doing a PhD in a respective field. However, do to some personal reasons I believe a remote studying situation would be the best fit for me. Is there any university where this could be possible?

Hi all, I've gotten involved in a project where we intend to predict in essence the forced degradation of organic substances by chlorination, amination, chloramination, and ozonation.

Ideally, I'd love to find some piece of software that takes an organic structure, and I can say "what happens if this is heated in the presence of water and chlorine?" Extra points if it's either free, or produced by a company which might work with industry and consultancies on favorable license terms. Extra-extra points if it actually predicts something close to reality ;)

Any ideas? I'm a toxicologist, not a chemist, so while I can predict mammalian metabolism, this type of thing is outside of my knowledge base.

Many thanks for any help!

Hi folks, I have a question regarding the sign of the exchange and correlation energies in computations. My current understanding is that the exchange energy (which is a subset of correlation energy) arises from interactions between electrons that share the same spin, and essentially says that there is a stabilizing energy from the fact that two fermions in the same system can not occupy the same quantum numbers, thus they have reduced interactions with each other and so are stabilized. The correlation energy, as I understand it, is all of the other electron-electron interactions that are not electron exchange, including the effect of one electron on another from Coulomb repulsions. My confusion is about how during computations that I have run, the correlation energy is also a stabilizing energy, since I would have assumed that Coulomb repulsion and the other terms in there seem like they would be destabilizing?

I tried looking through some textbooks like the Messiah Quantum Mechanics book, and the classic Szabo and Ostlund, but I have yet to find anything that talks about stabilizing energy versus destabilizing energy.

Can't afford Maestro... I've used GMMX but it's so clunky and only MMFF... I don't trust Spartan... What other options are there out there?

[Edit] Thanks for the suggestions. I'm going to be using the resulting conformers to generate 13C NMR shifts.

Hello! I'm trying to use PySCF to calculate the exchange correlation potential from an unrestricted kohn sham calculation so that I can use it in a scf loop that I am trying to implement myself.

I have been trying to this by the code below where I understand vxc contains vrho and vsigma terms. How does pyscf then combine these to calculate the potential for a GGA functional like pbe and update the electron density in a scf step?

exc, vxc, fxc, kxc = dft.numint.NumInt().eval_xc(
    "pbe", 
    (rho_up, rho_down), 
    deriv = 1, 
    spin = 1
)

I'm a 19m doing an undergrad in chemical engineering technology, which is not as prestigious as a bachelor of science in chemical engineering. I used to be a straight A's student in highschool but got into the wrong stuff through peer pressure and ended up graduating highschool with a grade B average but got a B+ in chemistry and A in mathematics. Is it too late too start a career in computational chemistry and if not, how should I do it??

I really need this

Hey there , I want a help for running my dft study on a métal complexe compound, using gauss 09, but it stops always ifter some time (2 days or more )

Dear everyone, thank you for reading this post.

Recently, I was trying to run some frequency calculations in ORCA 6.0.0 after the geometry had been optimized with the TightOPT keyword. I tried to tweak the input file a few times, but ORCA keeps returning this error message below. This error is returned after the SCF has converged. I will attach the input file structure to the comment.

-----------------------

GEOMETRIC PERTURBATIONS (xx nuclei)

-----------------------

MaxCore ... 8192 MB

Number of batches ... 15

BATCH 0: Atoms 0 - 4 ( 15 perturbations)

=> H(core) and overlap derivative integrals ... done ( 2.3 sec)

=> Making and storing internal U-coefficients ... done ( 0.7 sec)

=> RI-J derivative integrals ...

ORCA finished by error termination in PROPINT

Calling Command: mpirun -np 15 /software/apps/orca/6.0.0/orca_6_0_0/orca_propint_mpi inputfilename.propintinp.tmp inputfilename inputfilename

[file orca_tools/qcmsg.cpp, line 394]:

.... aborting the run

I appreciate any suggestions. Thank you all for being considerate to a beginner in compchem.