How to add Europium atomic parameter in autodock?

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How to handle the multiple read keywords in the Gaussian input?

Dear All, I am trying the calculate the ROA calculations on the isotopically labelled forms of a molecule. For ROA and for the selection of isoptopes, i need to specify the input frequency of...

31 December 2018 9,718 1 View

What is reason for the existing covalent bond broken effect while generating the molecular graph using AIM2000?

I am experiencing an error while generating the molecular graph using AIM 2000 Program. When I check from the .sum file, the critical point parameters corresponding to all the covalent bonds are...

07 August 2018 6,938 0 View

Why the bonds or trajectories between the non-bonded atoms in the AIM molecular graph is not straight?

In the atoms in molecules calculation, we get molecular graph which represents the bonds or trajectories between the non-bonded atoms. In some cases, the trajectories between the non-bonded atoms...

07 August 2018 1,023 0 View

What does the error "Two-electron integral symmetry is turned on." or "Two-electron integral symmetry is turned off." meant for in Gaussian output?

Dear All, when I optimize the structure without nosymm keyword, the job was terminated with the error "Two-electron integral symmetry is turned on". when I optimized the structure with nosymm...

01 February 2016 899 0 View

How to install NICplot in Windows?

I want to install NICplot in windows to calculate non-covalent interactions. Please anyone kindly assist me in this regard.

31 December 2015 5,789 0 View

Why does the NBO output of Gaussian doesn't give information about hydrogen bonding interactions within the molecule?

In the NBO output, it generally gives energies of n→σ* , σ→σ* interactions, etc. But it doesn't give the energies of hydrogen bonding interactions. Why?

08 September 2015 8,089 2 View

How can I draw 4D gaussian grid plot in Gaussian?

I have choosen three different dihedral angle coordinates for finding the conformational stability of a molecule. When i try to view gaussian grid plot, it shows the plot like a 2D plot (angle is...

06 July 2015 10,333 2 View

How do I find the canonical molecular orbital informations from Gaussian output file?

Dear All, i have gone through the gaussian nbo tutorials and i tried to find the orbital contributions in homo and lumo energy levels. But when i used $nbo cmo $end in the last line of the...

06 July 2015 9,348 16 View

How do we use the option "anharmonic corrections" in Gaussian 09W?

Here i have attached a file which shows the anharmonic correction option available in Gaussian 09W. But i don't know How do we use the option "anharmonic corrections" in Gaussian 09W? hoping to...

04 May 2015 6,927 2 View

How do we use the option "anharmonic corrections" in Gaussian 09W?

Here i have attached a file which shows the anharmonic correction option available in Gaussian 09W. But i don't know How do we use the option "anharmonic corrections" in Gaussian 09W? hoping to...

04 May 2015 9,095 3 View

1. If I can quantize the atom using this hyperbolic spiral and classical physics, could nature do the same?

If we map as a continuous motion an ionising electron (beginning its journey at n=1) in an H atom, a specific hyperbolic spiral appears (see animation). When we solve this spiral formula, we find...

07 August 2024 5,343 2 View

Gromacs first step of minimization ?

I have face this problem anyone help me how to solve this issue ?which is below Fatal error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 78 atoms. The...

07 August 2024 2,598 1 View

Should I include H atom into C3N5 when i am doing DFT modelling?

Hi all, my experimental XPS results shown that my C3N5 sample consists of N-H bond, hence in this case I should incorporate the N-H bond into my DFT modelling. However, I do notice several papers...

07 August 2024 8,414 2 View

Why reactivity isn't increased with more empty spots in valence shell?

If from a geometric perspective the non-halogens, non-noble gases have more empty spots in their valence shell, and the filling/exiting of any of the empty spots in the shell constitutes a...

03 August 2024 4,787 2 View

Why don't d-orbitals split themselves, why does it take a ligand? why don't protons from ligand repel nucleus split d-orbitals?

why don't d-orbitals split themselves because of themselves without the presence of ligands? Electrons are indistinguishable. Why wouldn't it be more correct that protons from a ligand split the...

03 August 2024 3,589 3 View

Why doesn't chromium 2+ ion use all its d-orbitals to receive lone pairs from six waters in [Cr(H20)6)]3+?

I'm guessing it's because the ligand experiences too much electron repulsion or proton repulsion from the chromium to insert them close to the 3d-orbitals which are close to the metal nucleus. Is...

03 August 2024 1,370 1 View

Why do paired electrons atoms produce no magnetic field lines?

If you think of electrons with spin as bar magnets, you know bar magnets of opposite polarity as long as they're not occupying the same spatial location don't cancel out each other's magnetic...

03 August 2024 3,927 2 View

How can you draw a coordinate bond between a metal and donor atom in metal complexes, using discovery studio visulizer software?

Hello,, The metal complex ligand appears incomplete in the screen of the discovery studio visualizer

30 July 2024 3,354 1 View

How to do pca analysis of c-alpha atom of the protein?

i m interested in pca analysis of c-alpha atoms in gromacs for that i used the following gmx_mpi covar -s mdca.tpr -f mdca.xtc -o eigenvalca.xvg -v eigenvecca.trr -av average.pdb -n index.ndx but...

30 July 2024 1,607 1 View

AutoGrid and Autodock 4.2.6 window opens for 1 second then closes and there is no output files?

Good day, I am a student trying to work on Autodock for a project regarding Ligand-DNA interaction so i am quite new to molecular docking. i have followed tutorials and did all the steps...

28 July 2024 2,136 4 View

Mohammad Tarek

you can just add the parameters to the force field prarameter file manually as shown here

http://autodock.scripps.edu/faqs-help/faq/where-do-i-set-the-autodock-4-force-field-parameters

atom_par Eu 3.49 0.008 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding

Karthick Thangavel

Thank you so much.