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Questions related to Atoms
Here, a ligand search is done to get the CGENFF force field for serotonin. But the atom type is mismatched.
Hello,
I hope that my question is not too obvious but I can't find a satisfying answer. I'm studying a very simple box of 8000 Argon atoms in a Lennard-Jones potential. I want to study many different samples to then average over them. I was thinking of using one equilibration of the system (NVT) and then running it for some time, and using this as my second equilibrated system. My question is: how long should I run the equilibration again for them to be decorrelated in time ? I was thinking 50ps, but I would like something optimal. Thank you for your answers.
I am trying to run MD calculations with an RNA aptamer in Amber. The first step (detachement of hydrogens) occurs fine:
pdb4amber -y -i 7kd1.pdb -o apt-nh.pdb
However, this command gives the message:
"The following residues had alternate locations: U_21"
Than, I go with a command @tleap -f leaprc.RNA.OL3@ which works fine.
Than I print:
rec=loadpdb apt-nh.pdb
which results in:
Created a new atom named: P within residue: .R<G5 1>
Created a new atom named: OP1 within residue: .R<G5 1>
Created a new atom named: OP2 within residue: .R<G5 1>
Created a new atom named: OP3 within residue: .R<G5 1>
total atoms in file: 1914
Leap added 961 missing atoms according to residue templates:
961 H / lone pairs
The file contained 4 atoms not in residue templates
I type:
set default PBRadii mbondi2
Finally, I try to generate a topology file "saveamberparm rec apt.prmtop apt.inpcrd", which results in:
Warning: The unperturbed charge of the unit (-88.000000) is not zero.
FATAL: Atom .R<G5 1>.A<P 33> does not have a type.
FATAL: Atom .R<G5 1>.A<OP1 34> does not have a type.
FATAL: Atom .R<G5 1>.A<OP2 35> does not have a type.
FATAL: Atom .R<G5 1>.A<OP3 36> does not have a type.
Error: Failed to generate parameters
Warning: Parameter file was not saved.
However, when I look through the pdb file I cannot see abnormalities or missing atom types. So what is wrong with my pdb file (attached)?
Dear colleagues, I am aware of the differences between the RHF and UHF approximations. In RHF the same orbitals are used for the alpha and beta spin electrons, and the unpaired electron will be at the HOMO orbital, while in the UHF calculations different sets of orbitals are calculated for the alpha and beta spin electrons.
In an RHF calculation the free valence e.g. in an OH radical will be 1 on the oxgen atom and 0 on the hydrogen atom, the spin population will be 1 on the oxygen and 0 on the hydrogen atom. The spin density will be, however, 0 on both atoms, as the same orbitals are used for both spins. In the UHF approximation, however (using 4-31G orbitals, at the optimized UHF geometry the three valences are 1.005 on the oxygen and 0.004 on the hydrogen, the Mulliken spin populations are 1.05988 and -0.05988 on O and H atoms respectively, the spin densities are 0.1954493 and -0.0289111 on the oxygen and hydrogen atoms.
My question is as follows: if, e.g. we want to calculate spin densities for EPR hyperfine constants, is it possible at all to use the RHF approximation, which gives free valence but zero spin density, or only the UHF approximation? I know that RHF calculations are faster and simpler, and I also heard the the UHF functions are "spin contaminated" but I am not quite sure how is it related the above problem?
Looking forward to your comments.
Interference between two levels occurs through this contraction that occurs to space-time, and therefore, if we assume that the electron is in the third level, such as the sodium atom, and according to de Broglie’s law, the third level needs 3 ripples, so if a contraction occurs from the higher level until it interferes with the electron level, such as level 4 It is in the form of 3 ripples, and if there is interference from level 6 with the electron level, which is in level 3, it occurs in the form of 3 ripples, but the difference is that level 6 is the ripple amplitude (vibration amplitude) is higher than level 4.
About materials properties of BST (BaSrTiO3) and STO (SrTiO3)
Hi all,
Thanks for taking the time to help me. I have generated a charged oligomer chain using acepype, as it is the only software I have been able to find to automatically parametrize using the OPLS-AA force field. However, the output file indicates that there are atoms that it could not define. I have attached the files for further clarity. Would it be enough to define these groups by hand, assigning them to the functional groups that suit them best in the topology file with this force field?
I am attempting to repair missing atoms in two protein structures (PI3KR1 and PI3KCA; PDB IDs: 4JPS and 7PG5) using AutoDock Tools for an upcoming molecular docking study. However, I keep encountering an error (see attached image) and have been struggling to resolve this for several days. Can anyone provide assistance?
I want to do xrd rietveld refinement by using X'pert Highscore Plus program.
When execute search and peak, In my quality I don't have 'skip without the structure pattern'.
1. Why my program doesn't have skip without the structure pattern?
2. When doing rietveld refinement using reference, it didn't detect 'no valid atom position available'
X'pert Highscore Plus - v 3.00
I have database, I don't know the problem....
Please help....
Dear all
i want to opt my complex with mp2 (6-311++g(d,p)) for C H N O atoms and GenECP (lanl2dz) for Zn atom. but i encounter this error:
Rotational constants (GHZ): 1.2999882 0.4336825 0.3251961
General basis read from cards: (5D, 7F)
QPErr --- A syntax error was detected in the input line.
'
Last state="Top"
TCursr= 927 LCursr= 0
Error reading general basis specification.
Error termination via Lnk1e in /opt/g09/g09/l301.exe at Sat Oct 26 22:20:20 2024.
Job cpu time: 0 days 0 hours 0 minutes 0.3 seconds.
File lengths (MBytes): RWF= 27 Int= 0 D2E= 0 Chk= 2 Scr= 2please
please suggest a solution and just do not link to gaussian error messages since i read it
here i attach the input file.
thanks guys
How does the substrate atom hold the sample atoms on the film?
Hello, everybody. I am an undergraduate student. I have tried calculating the [4Fe-4S] cluster's energy and frequency using the Gaussian program. But the problem is that the program does not recognize sulfur from the cytidine, even though I removed the sulfur to make it an ion. How do I calculate it? How do I make the input structure? How to insert the sulfur atom?
Thank you.
Using Gaussian, I tried to check the Total Energy of the 4-valent atom. I found that the energy of the neutral atom was calculated, but the Total energy of the 4-valent atom was derived as a blank. I don't know why. Which variable should I adjust? I have attached some calculation results to show the situation. I need help.
Interference between two levels occurs through this contraction that occurs to space-time, and therefore, if we assume that the electron is in the third level, such as the sodium atom, and according to de Broglie’s law, the third level needs 3 ripples, so if a contraction occurs from the higher level until it interferes with the electron level, such as level 4 It is in the form of 3 ripples, and if there is interference from level 6 with the electron level, which is in level 3, it occurs in the form of 3 ripples, but the difference is that level 6 is the ripple amplitude (vibration amplitude) is higher than level 4.
I want to simulate polymer in water for that I have confusion in reduce units according my understanding of reduce units if we perform simulation in reduce units means we are make a generalize model because we set sigma , Ellison, mass and other bonding parameters equal to one means we are simulating not real model.
It's like we are doing simulation of ball and spring model.
My confusion is regarding parameter that is equal to one or not for all atoms?
what is benifit of doing molecular simualiton in reduce units especially if have moleuclar like dna or potein where are so many different atoms??
There are 4 samples that deposited different process times. Xrd datas of them are different (shows different phases and different atomical rates of elemental compounds). But, Raman analyzes of them stayed same. Is that possible?
2) How is the formation of the universe?
The universe, at its most fundamental level, appears to operate according to the principles of quantum mechanics, where uncertainty and indeterminacy play key roles in shaping its evolution. In classical computational theory, Turing’s Halting Problem demonstrates that it is impossible to predict whether a system will reach a final state or run indefinitely. This raises profound questions about the nature of the universe: could it, too, one day halt, reaching a state where no further evolution is possible? However, the inherent unpredictability of quantum mechanics—through phenomena like superposition, quantum fluctuations, and entanglement—may offer a safeguard against such a scenario. This paper explores the intersection of quantum mechanics and the Halting Problem, suggesting that quantum uncertainty prevents the universe from settling into a static, final state. By continuously introducing randomness and variation into the fabric of reality, quantum processes ensure the universe remains in perpetual motion, avoiding a halting condition. We will examine the scientific and philosophical implications of this theory and its potential to reshape our understanding of cosmology.
Stam Nicolis added a reply:
The evolution of the universe, from the inflationary epoch onwards, is described by classical, not quantum, gravity.
Stam Nicolis added a reply:
Turing's halting problem doesn't have anything to do with the subject of cosmology, or any subject, where the equations that describe the evolution of the system under study are known.
In particular the answer to the question of the evolution of the universe is known: It's described by the de Sitter solution to Einstein's equations, that is its expansion is accelerating, although with a very slow rate. The question, whose answer isn't, yet, known is what happened before the inflationary epoch. It is for this question that a new theory is needed, that can match to classical description of spacetime and the quantum description of matter that emerged from it.
Stam Nicolis added a reply:
That quantum mechanics provides a probabilistic description isn't particular to it. Classical mechanics, also provides a probabilistic description, since classical systems are, typically, chaotic and integrable systems are the exception, not the rule. The only difference between a quantum system and its classical limit is the space of states.
Dale Fulton added a reply:
Turing's Halting Problem comes from computer sciences and the study of such systems. The question is whether nature obeys any of our "halting" knowledge and our myopic perspective of the universe. Likely not.
Javad Fardaei added a reply:
Dear Abbas We must realize that our universe is a complete entity that it is running billions of galaxies and place billions solar systems in each galaxy in most accurate way is not result of accident big bang, or run mechanically as our past icons (quantum mechanics, or any mechanical entanglement) stated it. Our universe like anything else (inside of it) has born and it has a natural journey. If you accept this fact, then we are in right track as far as knowing intelligent atom, not mechanical atom.
Unfortunately science believes someone imagination of collapsing our mechanical physics into nature (atom)
Reading this unprecedented articles might help your view of this magnificent universe of ours.
1-Article Universe's Rotation and Its Benefit:
2-Article Intelligent Atom:
Question:
I am performing thermochemistry calculations on organic molecules to investigate carbon stability in anoxic systems, focusing on the Gibbs free energy of oxidation per carbon atom (ΔGOx/C) for redox half-reactions. This is based on the work of LaRowe and Van Cappellen (2011) (DOI: 10.1016/j.gca.2011.01.020), and I am using Gaussian with the setup: # B3LYP/6-311+G(2d,p) Opt Freq SCRF=SMD.
My goal is to calculate the Gibbs free energy of oxidation for the redox half-reaction (not the full oxidation) per carbon atom, and I am working with a large dataset of over 4000 molecules. I have been using two different methods to obtain ΔGOx/C, but I am facing significant discrepancies in my results compared to the literature.
Here are the two methods I am using:
- Formation Energy Method:Step 1: I calculate the atomization energy of each molecule by summing the computed energies of its constituent atoms and subtracting the total energy of the molecule at 0 K, including zero-point energy (ZPE). Step 2: Using standard tables, I obtain the heats of formation for each atom, and then calculate the heat of formation for the molecule at 0 K. Step 3: I apply enthalpy corrections to adjust these values from 0 K to 298.15 K. Step 4: I compute the entropy for each molecule at 298 K and use this to calculate the Gibbs free energy of formation at 298 K. Step 5: I then apply the oxidation half-reaction equation for organic molecules (where products are HCO3(-), NH4(+), HS(-), HPO4(-2)) and compute the Gibbs free energy of oxidation (ΔGOx) for the redox half-reaction as Σ(ΔGproducts) − Σ(ΔGreactants). Finally, I divide this value by the number of carbon atoms to obtain the Gibbs free energy of oxidation per carbon atom (ΔGOx/C). Problem: Despite following these steps, the ΔGOx/C values I obtain deviate significantly from those reported in the literature. For example, my result for glucose is 90.76 kJ/molC, whereas the literature (LaRowe and Van Cappellen, DOI: 10.1016/j.gca.2011.01.020) reports approximately 65 kJ/molC. This deviation seems to be more prominent for molecules with non-neutral charges.
- GIE Method (Gaussian Internal Energy Method):Step 1: For each molecule (both reactants and products in the half-reaction), I perform a DFT geometry optimization and frequency calculation using B3LYP/6-311+G(2d,p) Opt Freq SCRF=SMD. Step 2: I sum the electronic and thermal Gibbs free energies directly from the Gaussian log files. Step 3: I use the same oxidation half-reaction equation as in the Formation Energy Method to calculate ΔGOx. I then divide by the number of carbon atoms to get ΔGOx/C. Example (For glucose):The half-reaction is: C6H12O6 + 12H2O → 6HCO3(-) + 24e(-) + 30H(+). Using the GIE method, I get the following Gibbs free energies from Gaussian:ΔG_HCO3(−) = -264.67 Hartree ΔG_H(+) = -0.41897 Hartree (from literature: DOI: 10.1016/j.molliq.2020.114919) ΔG_H2O = -76.47 Hartree ΔG_C6H12O6 = -687.29 Hartree The total Gibbs free energy for the reaction (ΔGOx) is calculated as: ΔGreaction=([6×(−264.67)+30×(−0.41897)]−[−687.29+12×(−76.47)])×2625.5=11421.3 kJ/mol\Delta G_{\text{reaction}} = \left( [6 \times (-264.67) + 30 \times (-0.41897)] - [-687.29 + 12 \times (-76.47)] \right) \times 2625.5 = 11421.3 \, \text{kJ/mol}ΔGreaction=([6×(−264.67)+30×(−0.41897)]−[−687.29+12×(−76.47)])×2625.5=11421.3kJ/mol Dividing by 6 (the number of carbon atoms in glucose) gives ΔGOx/C = 1903.55 kJ/molC. Problem: The ΔGOx/C values I obtain using this method are much larger than expected, often about 26.4 times higher. For glucose, my ΔGOx/C = 1903.55 kJ/molC, whereas the literature reports ~65 kJ/molC. Interestingly, when I apply an empirical scaling factor of 26.4, my results align closely with the literature (R² = 0.91), but I cannot explain why this factor is necessary.
Key Issues:
- Large deviations in the calculated ΔGOx/C for the redox half-reaction using both methods, with GIE method values being consistently about 26.4 times too large.
- The unexplained empirical scaling factor (26.4) that aligns the GIE results with the literature.
- Uncertainty about whether B3LYP/6-311+G(2d,p) Opt Freq SCRF=SMD is appropriate for calculating ΔGOx/C for redox half-reactions or if a different method would yield more accurate results.
- The need for a computationally efficient method, given the large dataset of over 4000 molecules.
Questions:
- What could be causing the large discrepancies and the unexplained scaling factor (26.4) in my ΔGOx/C values for the redox half-reaction?
- Is there a more appropriate computational method (functional/basis set) for calculating ΔGOx/C in these half-reactions that balances accuracy and computational efficiency?
- Could these issues stem from the way I am interpreting and processing the thermodynamic data from Gaussian, or might they be related to the specific setup of the redox half-reaction?
I’ve consulted Gaussian support, but the help they can provide is limited to software usage. I would appreciate any advice or suggestions on how to resolve these discrepancies and improve the accuracy of my calculations.
Thank you for your time and any insights you can offer!
How Penrose - Hameroff theory is crucial to answer this question?
In an intermetallic phase like Ni3Al, each Al is surrounded by 12 Ni atoms.
So for a dilute Ni alloy with a small concentration of Al atoms, it cannot be nearest neighbour interactions that are responsible for the formation of the phase because in solid solution, each Al is also surrounded by 12 Ni neighbours.
This means that next-nearest neighbour interactions must be responsible for this.
What exactly are these effects? Is it a delocalization of electrons in orbitals that are different when there are Al-Ni-Al chains?
Is it an effect of the density of states, although an intermetallic phase and a solid solution only differ in the fourth moments of the local DOS (4-step hops are the first to be different, with Al-Ni-Al-Ni being possible in the intermetallic, but not in the dilute solution)?
Is there a clear physical picture of this?
Dear researchers,
Very recently, I have downloaded the last version of IGMPlot, version 3.08.
I found some new descriptors included in this very nice, complete, and versatile version.
One of newly proposed descriptors is "qg" which makes 2-D plots colored based a given scale ranging from 1 (blue color) to 4 (red color). Please let me know the exact and straightforward meaning of these numbers and colors. Indeed, what is the practical usage of "qg" index? or, what is its interpretation when a given inter- or intra-fragment interactions is analyzed? I cannot understand what concept should be taken into account when a 2-D plot of delta_g_inter versus sign (lambda2*Rho) is colored from blue to red (from number 1 to 4). What practical information one can obtain depending on the color type of a given picke.
For instance, a taller picke (a larger delta_g value) means a stronger interaction but what statement should be provided for a smaller (blue) or greater (red) value of "qg"?
In advance, too many thanks for any help.
Best,
Saeed
i am currently working on Density of States (DOS) calculations for a nanocluster consisting of 99 atoms and 370 bands using VASP. In my setup, I am using a cluster with 40 cores distributed across 2 nodes, with 20 cores per node. The calculation is configured to run at the gamma point with a 1x1x1 k-point grid. I am executing the job with the following command:(mpirun -np 8 vasp_std)
However, despite these settings, my calculations either get stuck or stop without completing. I am particularly concerned about optimizing the parallelization tags such as NBANDS, NCORE, and others to ensure that the calculation runs efficiently and successfully. Specifically, I am interested in the best approach to parallelize over bands to utilize the available computational resources effectively?
As I know how to do refinement of pure sample by Fullprof software, how should done perform the refinement when doping is done into the pure sample, where substitution doping occurs. My concerns are:
1) Whether should I refine the whole doped sample by not incorporating the doped compound in atoms section in the Fullprof software and at last incorporate it (i.e. without adding the doped atoms and just doing a normal refinement of a pure compound)
or
2) When the cif file is added, then in the atoms section should I add them before performing the refinement.(I tried this way but was getting scattering errors).
3) What changes must be done, like in atoms does x,y and z changes or just the occupancy part changes. Say for example the occupancy is 0.4912 of A atoms and one is doing, say 10% of B atoms such that it will replace A atoms, so does A occupancy becomes then 0.44208 and B atoms occupancy as 0.04912 and what about its x y and z parameters?
What happens inside the atom?!
I'm trying to simulate molecular docking with the help of autodocktools. I have added all hydrogens to the protein, computed charges and assigned AD4 type, and the pdbqt file was saved. After that, I adjusted the parameters of grid box and output a gpf file successfully. However, when I run autogrid, the software interface suddenly disappeared and the cmd reported an error: Too many atoms in receptor PDBQT file......the maximum number of atoms, AG_MAX_ATOMS, allowed is 32768...... Sorry, AutoGrid cannot continue. So I want to know whether there is a method to increase the allowed maximum atoms of autodock? Or should I adjust the number of hydrogens or give up this protein? Thanks you!
Hi,
I am currently screening more than 2000 compounds virtually on Vina, but I would like to perform covalent docking. Unfortunately, Vina's functionality is limited as its requires manual designation of the reactive atoms on the ligands. Is there any alternative that is free for academic purposes and suited for this sort of task?
In a supercom with 40 cores/node, normally when I run VASP for a large system with a few hundreds atoms, I set NCORE=20 expecting that 20 cores treat 1 band inside node. Is it OK to apply the same INCAR setting for NEB calculation? When I run with 8 images, I found that all the 8 directories run at the same time. Then, what is happening here? 20 cores for 1 band is applied to 8 calculations at the same time, or do I need to change NCORE if I expect the same performace?
After performing the molecular docking of ligands containing chlorine atoms, the .pdb files of the complex of the conformers of interest and the respective receptor were generated from the .dlg.pdb output file using the Maestro program. When trying to visualize ligand-receptor interactions, Discovery Studio shows alkyl-type interactions with the chlorine atom.
Does anyone know how this error can be fixed?
Dear All,
I have come across something strange while doing RMSD calculation.
I calculated the RMSD of a mutated protein using the .tpr file generated from Wild type and it does the calculation without any error. Both the systems have different number of atoms and I was anticipating an error, but that didnt happen. Infact, I tried the calculation using totally unrelated .tpr from a different protein and yet it prints some values.
Now I'm totally confused about whats happening. I tried the calculation using two versions of gromacs:2020.2 and 2022 as well.
Can anyone explain what might have gone wrong here ? Or am I making some mistake in understanding.
Thanks and Regards
I'm trying to cyclise the molecule attached and am having trouble when using methods described for similar looking things. I ran a computational model that suggested that at their closest point, the 2 carbons I am trying to form a bond between are 6 Å apart, which is obviously quite far. So I have 2 questions really, 1) how close would the carbons need to be to each other to be able to form a bond (is it just around 1.54 Å, the bond length of a C-C bond)?
2) Are there ways to force these closer together together?
I am trying to find the thermal conductivity of a material with 3 atoms kinds through the Green-Kubo method. I could find the LJ pair coefficients of the material in any literature or database. I tried to estimate the values with Lorentz-Berthelot mixing rules but the obtained thermal conductivity with those parameters is much less than the experimental values.
Hello,
I'm trying to create parameter and coordinate files for a drug (PRG-A01) found on the following page:
I used the guide made by Michael Barton and Tyler Luchko at the following link: https://ambermd.org/tutorials/basic/tutorial4b/index.php
At first, I obtained the sdf structure thanks to the PDB Chemical sketch tool and converted into pdb using MOE (I simply did a quick prep and saved as pdb):
HEADER
REMARK 99
REMARK 99 MOE v2022.02 (Chemical Computing Group ULC) Thu Jul 18 15:08:13 2024
HETATM 1 O1 * 0 -16.219 1.636 -1.486 1.00 0.00 O1-
HETATM 2 C2 * 0 -16.359 1.987 0.839 1.00 0.00 C
HETATM 3 C3 * 0 -15.215 1.727 1.387 1.00 0.00 C
HETATM 4 C4 * 0 -14.286 1.316 0.345 1.00 0.00 C
HETATM 5 C5 * 0 -14.732 1.265 -1.013 1.00 0.00 C
HETATM 6 O6 * 0 -18.237 2.364 -0.412 1.00 0.00 O1-
HETATM 7 C7 * 0 -13.868 0.878 -2.019 1.00 0.00 C
HETATM 8 C8 * 0 -12.967 0.968 0.644 1.00 0.00 C
HETATM 9 C9 * 0 -12.095 0.571 -0.368 1.00 0.00 C
HETATM 10 C10 * 0 -12.557 0.538 -1.694 1.00 0.00 C
HETATM 11 O11 * 0 -11.720 0.155 -2.719 1.00 0.00 O
HETATM 12 C12 * 0 -10.666 0.191 -0.042 1.00 0.00 C
HETATM 13 C13 * 0 -10.048 -0.656 -1.169 1.00 0.00 C
HETATM 14 C14 * 0 -10.295 -0.012 -2.565 1.00 0.00 C
HETATM 15 O15 * 0 -8.647 -1.082 -0.914 1.00 0.00 O
HETATM 16 C16 * 0 -7.582 -0.324 -0.570 1.00 0.00 C
HETATM 17 C17 * 0 -3.884 -0.967 0.266 1.00 0.00 C
HETATM 18 C18 * 0 -2.759 -0.142 0.425 1.00 0.00 C
HETATM 19 C19 * 0 -3.711 -2.361 0.368 1.00 0.00 C
HETATM 20 C20 * 0 -2.456 -2.913 0.611 1.00 0.00 C
HETATM 21 C21 * 0 -1.348 -2.080 0.760 1.00 0.00 C
HETATM 22 C22 * 0 -1.503 -0.685 0.667 1.00 0.00 C
HETATM 23 C23 * 0 -17.053 2.034 -0.313 1.00 0.00 C2+
HETATM 24 O24 * 0 -0.472 0.237 0.803 1.00 0.00 O
HETATM 25 C25 * 0 0.938 -0.002 1.045 1.00 0.00 C
HETATM 26 O26 * 0 -0.128 -2.662 0.996 1.00 0.00 O
HETATM 27 O27 * 0 -7.741 0.878 -0.488 1.00 0.00 O
HETATM 28 C28 * 0 -6.328 -1.001 -0.330 1.00 0.00 C
HETATM 29 C29 * 0 -5.180 -0.349 0.009 1.00 0.00 C
HETATM 30 C30 * 0 -9.657 1.367 -2.812 1.00 0.00 C
HETATM 31 C31 * 0 -9.841 -0.960 -3.684 1.00 0.00 C
HETATM 32 H1 * 0 -15.058 1.822 2.431 1.00 0.00 H
HETATM 33 H2 * 0 -14.215 0.846 -3.017 1.00 0.00 H
HETATM 34 H3 * 0 -12.658 1.015 1.655 1.00 0.00 H
HETATM 35 H4 * 0 -10.648 -0.384 0.884 1.00 0.00 H
HETATM 36 H5 * 0 -10.104 1.111 0.115 1.00 0.00 H
HETATM 37 H6 * 0 -10.621 -1.586 -1.176 1.00 0.00 H
HETATM 38 H7 * 0 -2.853 0.911 0.359 1.00 0.00 H
HETATM 39 H8 * 0 -4.540 -3.012 0.267 1.00 0.00 H
HETATM 40 H9 * 0 -2.348 -3.965 0.684 1.00 0.00 H
HETATM 41 H10 * 0 1.472 0.947 1.100 1.00 0.00 H
HETATM 42 H11 * 0 1.369 -0.595 0.238 1.00 0.00 H
HETATM 43 H12 * 0 1.079 -0.533 1.988 1.00 0.00 H
HETATM 44 H13 * 0 -0.168 -3.639 1.036 1.00 0.00 H
HETATM 45 H14 * 0 -6.360 -2.051 -0.440 1.00 0.00 H
HETATM 46 H15 * 0 -5.204 0.711 0.095 1.00 0.00 H
HETATM 47 H16 * 0 -9.951 2.073 -2.035 1.00 0.00 H
HETATM 48 H17 * 0 -10.009 1.765 -3.764 1.00 0.00 H
HETATM 49 H18 * 0 -8.571 1.298 -2.846 1.00 0.00 H
HETATM 50 H19 * 0 -8.762 -1.107 -3.654 1.00 0.00 H
HETATM 51 H20 * 0 -10.117 -0.544 -4.654 1.00 0.00 H
HETATM 52 H21 * 0 -10.340 -1.924 -3.580 1.00 0.00 H
CONECT 1 5 23
CONECT 2 3 3 23
CONECT 3 2 2 4 32
CONECT 4 3 5 5 8
CONECT 5 1 4 4 7
CONECT 6 23
CONECT 7 5 10 10 33
CONECT 8 4 9 9 34
CONECT 9 8 8 10 12
CONECT 10 7 7 9 11
CONECT 11 10 14
CONECT 12 9 13 35 36
CONECT 13 12 14 15 37
CONECT 14 11 13 30 31
CONECT 15 13 16
CONECT 16 15 27 27 28
CONECT 17 18 19 19 29
CONECT 18 17 22 22 38
CONECT 19 17 17 20 39
CONECT 20 19 21 21 40
CONECT 21 20 20 22 26
CONECT 22 18 18 21 24
CONECT 23 1 2 6
CONECT 24 22 25
CONECT 25 24 41 42 43
CONECT 26 21 44
CONECT 27 16 16
CONECT 28 16 29 29 45
CONECT 29 17 28 28 46
CONECT 30 14 47 48 49
CONECT 31 14 50 51 52
CONECT 32 3
CONECT 33 7
CONECT 34 8
CONECT 35 12
CONECT 36 12
CONECT 37 13
CONECT 38 18
CONECT 39 19
CONECT 40 20
CONECT 41 25
CONECT 42 25
CONECT 43 25
CONECT 44 26
CONECT 45 28
CONECT 46 29
CONECT 47 30
CONECT 48 30
CONECT 49 30
CONECT 50 31
CONECT 51 31
CONECT 52 31
END
Then I used the following instructions adapted from the guide:
obabel PRG_A01.pdb -O PRG_A01_h.pdb -h
antechamber -i PRG_A01_h.pdb -fi pdb -o PRG_A01.mol2 -fo mol2 -c bcc -s 2
parmchk2 -i PRG_A01.mol2 -f mol2 -o PRG_A01.frcmod
tleap
source leaprc.protein.ff19SB
source leaprc.gaff
PRG = loadmol2 PRG_A01.mol2
loadamberparams PRG_A01.frcmod
saveoff PRG PRG_A01.lib
saveamberparm PRG PRG_A01.prmtop PRG_A01.rst7
The PRG_A01.frcmod file when opened gives:
"Remark line goes here
MASS
BOND
ANGLE
DIHE
IMPROPER
NONBON"
So I don't know if the line of instruction "parmchk2 -i PRG_A01.mol2 -f mol2 -o PRG_A01.frcmod" did properly its job.
Furthermore this is what each instruction returned.
[marco99@narval2 PRG_A01 preparation]$ obabel PRG_A01.pdb -O PRG_A01_h.pdb -h
[mii] Please select a module to run obabel:
MODULE PARENT(S)
1 openbabel/3.1.1 StdEnv/2023 gcc/12.3
2 openbabel-omp/3.1.1 StdEnv/2023 gcc/12.3
3 openbabel/3.1.1 StdEnv/2020 intel/2020.1.217
4 openbabel-omp/3.1.1 StdEnv/2020 intel/2020.1.217
5 gnina/1.0.1 StdEnv/2020 gcc/9.3.0 cuda/11.0
6 openbabel/3.1.1 StdEnv/2020 gcc/9.3.0
7 openbabel-omp/3.1.1 StdEnv/2020 gcc/9.3.0
Make a selection (1-7, q aborts) [1]: 1
[mii] loading StdEnv/2023 gcc/12.3 openbabel/3.1.1 ...
Lmod is automatically replacing "boost-mpi/1.82.0" with "boost/1.82.0".
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
The following dependent module(s) are not currently loaded: boost-mpi/1.82.0 (required by: amber/22.5-23.5)
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
1 molecule converted
[marco99@narval2 PRG_A01 preparation]$ antechamber -i PRG_A01_h.pdb -fi pdb -o PRG_A01.mol2 -fo mol2 -c bcc -s 2
Welcome to antechamber 22.0: molecular input file processor.
Info: acdoctor mode is on: check and diagnose problems in the input file.
Info: The atom type is set to gaff; the options available to the -at flag are
gaff, gaff2, amber, bcc, and sybyl.
-- Check Format for pdb File --
Status: pass
Info: Determining atomic numbers from atomic symbols which are case sensitive.
-- Check Unusual Elements --
Status: pass
-- Check Open Valences --
Status: pass
-- Check Geometry --
for those bonded
for those not bonded
Status: pass
-- Check Weird Bonds --
Status: pass
-- Check Number of Units --
Status: pass
acdoctor mode has completed checking the input file.
Running: /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
Running: /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Info: Total number of electrons: 222; net charge: 0
Running: /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/bin/sqm -O -i sqm.in -o sqm.out
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 0, Name: O1).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 1, Name: C2).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 2, Name: C3).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 5, Name: O6).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 5, Name: O6).
Automatically increasing to 15000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 5, Name: O6).
Automatically increasing to 20000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 17, Name: C18).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 17, Name: C18).
Automatically increasing to 15000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 18, Name: C19).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 19, Name: C20).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 20, Name: C21).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 21, Name: C22).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 22, Name: C23).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 23, Name: O24).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 24, Name: C25).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 25, Name: O26).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 31, Name: H1).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 37, Name: H7).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 37, Name: H7).
Automatically increasing to 15000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 38, Name: H8).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 39, Name: H9).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 40, Name: H10).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 41, Name: H11).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 42, Name: H12).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 43, Name: H13).
Automatically increasing to 10000.
Info: The number of path atoms exceeded MAXPATHATOMNUM for atom (ID: 52, Name: H).
Automatically increasing to 10000.
Running: /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/dat/antechamber/BCCPARM.DAT -s 2 -j 1
Running: /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC
[marco99@narval2 PRG_A01 preparation]$ ^C
[marco99@narval2 PRG_A01 preparation]$ parmchk2 -i PRG_A01.mol2 -f mol2 -o PRG_A01.frcmod
[marco99@narval2 PRG_A01 preparation]$ tleap
-I: Adding /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/dat/leap/prep to search path.
-I: Adding /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/dat/leap/lib to search path.
-I: Adding /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/dat/leap/parm to search path.
-I: Adding /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/dat/leap/cmd to search path.
Welcome to LEaP!
(no leaprc in search path)
> source leaprc.protein.ff19SB
----- Source: /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/dat/leap/cmd/leaprc.protein.ff19SB
----- Source of /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/dat/leap/cmd/leaprc.protein.ff19SB done
Log file: ./leap.log
Loading parameters: /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/dat/leap/parm/parm19.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA + ff19SB
Loading parameters: /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/dat/leap/parm/frcmod.ff19SB
Reading force field modification type file (frcmod)
Reading title:
ff19SB AA-specific backbone CMAPs for protein 07/25/2019
Loading library: /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/dat/leap/lib/amino19.lib
Loading library: /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/dat/leap/lib/aminoct12.lib
Loading library: /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/dat/leap/lib/aminont12.lib
> source leaprc.gaff
----- Source: /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/dat/leap/cmd/leaprc.gaff
----- Source of /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/CUDA/gcc12/openmpi4/cuda12.2/amber/22.5-23.5/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
> PRG = loadmol2 PRG_A01.mol2
Loading Mol2 file: ./PRG_A01.mol2
Reading MOLECULE named *
> loadamberparams PRG_A01.frcmod
Loading parameters: ./PRG_A01.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> saveoff PRG PRG_A01.lib
Creating PRG_A01.lib
Building topology.
Building atom parameters.
> saveamberparm PRG PRG_A01.prmtop PRG_A01.rst7
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
!FATAL ERROR----------------------------------------
!FATAL: In file [/tmp/ebuser/avx2/Amber/22.5-23.5/gofbc-2023a/AmberTools/src/leap/src/leap/unitio.c], line 1955
!FATAL: Message: 1-4: cannot add bond 2 3
This may be caused by duplicate bond specifications;
for example, explicit bond commands in addition to PDB conect records.
!
!ABORTING.
The last instruction "saveamberparm PRG PRG_A01.prmtop PRG_A01.rst7" gives the fatal error I'm worried about:
!FATAL ERROR----------------------------------------
!FATAL: In file [/tmp/ebuser/avx2/Amber/22.5-23.5/gofbc-2023a/AmberTools/src/leap/src/leap/unitio.c], line 1955
!FATAL: Message: 1-4: cannot add bond 2 3
This may be caused by duplicate bond specifications;
for example, explicit bond commands in addition to PDB conect records.
!
I tried to remove the conects and remarks from the PDB file of the structure (which MOE added), resulting in the same error.
Is there a ways to face this obstacle?
Thank you very much
Suppose i have two compounds H2O and H2O2 or CO and CO2, i want to make crystal how can i make in material studio?
I am using Materials Studio and the CASTEP software package. I would like to apply Hubbard U corrections to a model that includes transition metals. Should I directly adjust the Hubbard U values for the atoms in the "Electronic Configuration" section, and do I need to enable the LDA+U option during the calculations?
If I don't use LDA+U, will the system be unable to recognize the Hubbard U correction values?
Hello all,
I am trying to determine the dependence of the energy gap of silicon as a function of temperature. In the literature, it is stated that the decrease in the energy gap of silicon with increasing temperature can be explained by thermal expansion and electron-phonon interaction.
First, I used the thermo_pw library (which uses the QHA approximation) to determine the lattice parameter of silicon as a function of temperature. Then, I ran the following calculations: SCF, NSCF, DOS, band, and finally plotband. I performed these calculations using the lattice parameters of Si corresponding to temperatures in a range from 4K to 800K. For this simulation, I am using PBE pseudopotentials, an ecutwfc of 25 Ry, and a unit cell with 2 atoms.
The problem is that the gap increases with temperature instead of decreasing. I obtained a gap of 0.6187 eV at 4K and 0.6315 eV at 800K.
I also tried calculating the band structure considering electron-phonon coupling using the EPW library, but the gap still increases with temperature.
Has anyone already tried to calculate the silicon gap as a function of temperature? What am I doing wrong?
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 report N-H bond from their XPS results too but did not incorporate it into their modelling while some did include the N-H bond.
This confuses me, logically I feel like it should include the N-H bond so that the modelling is closer to the experimental case. However, is there any specific reason they do not include H-bond for modelling?
If we map as a continuous motion an ionising electron (beginning its journey at n=1) in an H atom, a hyperbolic spiral emerges (see animation). When we solve this spiral formula, we find that at regular intervals the spiral angles will cancel to give integer radius values (360°=4r, 360+120°=9r, 360+180°=16r, 360+216°=25r ... 720°=∞ ... formulas below).
As the orbital levels corresponding to the principal quantum number n^2 (4, 9, 16, 25 ...) naturally occur via this spiral geometry, then at those points where the angles cancel to give integer radii (360°, 360+120°, 360+180°, 360+216° ...) we can use the spiral perimeter (r = Bohr radius) to derive the transition frequency for that integer (n^2) level ......, thus equating these energy levels directly to pi, the question then becomes, could quantization in the atom have geometrical origins?
In the animation the radius is mapped (during ionization), as the electron reaches each integer level, it completes 1 orbit (for illustration) then continues outward (actual velocity will become slower as radius increases).
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 longest distance involved in such interactions is
4.894 nm which is above half the box length. Either you have excessively large
distances between atoms in bonded interactions or your system is exploding.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
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 chemical rxn, shouldn't non-halogens and non-noble-gases be more reactive? (AFAIK) Just from a probability perspective, the probability of hitting the empty spot in the electron shell which is crowded by 7 electrons already is just less likely when you can hit any of the >1 empty places in the shell of the electron accepting atom. I'm aware electrons are non-stagnant.
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 field.
So what's a more apt analogy/or math reason, or explanation for all electron paired atoms have no magnetic field?
I don't even know what the central atom of a isoprene is. Does the rule above work when you don't have an odd number of carbons on the longest not necessarily straight backbone?
Hello,, The metal complex ligand appears incomplete in the screen of the discovery studio visualizer
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 i am getting the error
Range checking error (possible bug):
The provided structure file only contains 10 coordinates, but coordinate index
147 was requested for fitting. Make sure to update structure files and index
files if you store only a part of your system.
how should i prepare the md.tpr file for only c-alpha atom
Can someone verify me whether its right or wrong the number of atoms displayed in Burai using same cif created by vesta?
We are currently trying to calculate the lattice thermal conductivity of several metals (Ni, Cu, Pd, Ag, Pt and Au) using the non-equilibrium Müller-Plathe method in LAMMPS. We are considering big supercells (20x20x20 unit cells, 70k+ atoms) for each elemental metal separately. The interactions between atoms are mediated by the well-known MEAM potential. The heat flux is tallied using the fix thermal/conductivity command, and temperature profiles are recorded using the compute chunk/atom and fix ave/chunk commands. Please find attached the typical input run for reference. We have successfully run this for other systems (molecular liquids governed by OPLS-AA), but for MEAM metals we found that the temperature profiles are basically erratic noise. While the lattice thermal conductivity of metals should low, we do not expect it to be completely negligible.
Is anyone aware of existing problems with the application of the Müller-Plathe method together with the MEAM potential? Is there particular requirements for such a case? We have played with the Nevery and Nswap parameters in the fix thermal/conductivity command with no success.
Thank you in advance for your attention.
*****
include "system.in.init"
read_data "system.data"
include "system.in.settings"
include "system.in.charges"
neigh_modify every 1 delay 0 check yes
variable t equal 0.001
variable T equal 298.0
variable P equal 1.013
variable s equal 5
variable c equal 10000
variable d equal $s*$c
variable kB equal 8.617333262E−5
minimize 1.0e-6 1.0e-8 1000 100000
reset_timestep 0
timestep $t
thermo_style custom step etotal temp press lx ly lz density
thermo 1000
fix 1 all nvt temp $T $T 10.0
run 500000
unfix 1
fix 2 all npt temp $T $T 10.0 iso $P $P 100.0
run 2000000
unfix 2
reset_timestep 0
thermo_style custom step etotal epair ke temp press
thermo 1000
fix 3 all nvt temp $T $T 10.0
run 10000000
unfix 3
reset_timestep 0
fix 4 all nve
fix 5 all thermal/conductivity 100 z 50
compute ke all ke/atom
variable temp atom c_ke/(1.5*${kB})
compute layers all chunk/atom bin/1d z lower 0.02 units reduced
fix MP all ave/chunk $s $c $d layers v_temp file temp.profile ave one
thermo_style custom step etotal epair ke temp press f_5
thermo 1000
run 10000000
unfix MP
unfix 5
unfix 4
Can we calculate the friction coefficient of an interface by only knowing the atom types and geometry forming it, without performing any experiment or simulations? We think yes, and discuss a possible route to get there in our recently published review - download it with this free access link
During the preparation of a ligand molecule in autodock or openbabel Cl atom is not showing in the .pdbqt file whereas it was present in the pdb and sdf file. Due to this Cl atom is not showing in the docked complex as well. How do we resolve this issue? I am attaching two images for your reference.
Thanks in advance
Hi, my research involves in ZnO synthesis. I have performed rietveld refinement of my samples and obtain a good fit using Fullprof suite software. However to obtain the crystallite size, the IRF file is required which often generated from the standards as LaB6, Si etc.,,, . May i know whether others standards (in my case, pure ZnO) be used to generate the IRF file since I have analyzed the pure ZnO sample with the same XRD instrument. I also have performed the rietveld refinement on the pure ZnO and obtain pretty much similar crystal parameter (lattice constants,...atom occupancies..etc.,,) with the standard ZnO sample from the cif files. Therefore, can i used the pure ZnO XRD pattern to generate the IRF file ?
My ligand is a metal complex conatining Ag (Silver). So when i tried to run Molecular docking using Autodock vina as well as PyRx, it shows error as
"Parse error on line 15 in file "Methioninesilver.pdbqt": ATOM syntax incorrect: "Ag" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive."
Any necessary recommendation to overcome this error.
The error message is "Angle parameter for atoms42-45-15 (cf-nu-ns) not found in the force field. Initialization is not possible, check atoms for incorrect bonds, then update the force field's angle parameter section".
What should I do to run the simulation after error correction
I am trying for the structure optimization via Gaussian16 DFT calculation, for a system consisting of C,H, N, O and Ce atoms. Where I am using B3LYP/ 6,311G(d,p) C, H, N and O and B3LYP/SDD for Ce. I am having error termination Error termination via Lnk1e in /share/apps/gaussian/g16/l502.exe
Any suggestion for normal termination?
Hello dear researchers, I hope you are doing well.
I want to ask you a question. I have a unit cell with 24 atoms (4 A, 4 B and 16 X) and I want to substitute X atom by another atom (for example changing one X by other element).
My question is, can I substitute it within the unit cell without making supercell?? or should I make a supercell??
Hello everyone, I am currently working on miRNA- mRNA interaction study. Further, I would like to do MD simulations for the miRNA-mRNA models.
For the Simulation, I have modelled this complex using the Alphafold server. But when I try to use AlphaFold models for the Gromacs MD simulations, it gives some error when I apply the force field (Amber - 2010).
The error is "Atom OP3 in residue U 1 was not found in rtp entry RU5 with 28 atoms while sorting atoms."
If I change the atom name, it shows another atom is missing (attached the screen shot with this Q&A)
Is there any updated force field or modelling algorithm?
Kindly help me to solve this issue.
I am trying to run a md stimulation in gromacs for HDAC2 inhibitor and ligand. The protein is metalo protein, contain a Zn atom. Now I am facing problem while converting the pbd to gmx, i.e., in the time of applying forcefield. I have attached the error details. It will be very helpful if anyone can solve this error.
I encounter an issue in Vista; the system fails when determining the atoms ?
Suppose a lab experiment gave evidence that the DNA or RNA code for bacteria are stored in radioactive chemical atoms, because the atomic decays are followed by the appearance of protozoa in a test tube of sterile chemical building blocks. Would this be an evidence for a cosmic mind that formed the atoms containing these genetic codes?
I am working on a molecular dynamics simulation in protein-ligand system, using NAMD software, and I got the following error.
"FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HGA1 CG3C51 SG311 (ATOMS 1753 1752 1770)"
The atoms mentioned above belong to the ligand structure. The .str and topology files for the ligand were generated using Charmm-gui. Can someone help me to solve this failure? Thank you in advance.