Questions tagged [software]
For questions pertaining to software used by chemists for professional or academic purposes.
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2answers
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How To Scan “improper dihedrals” in Gaussian 09?
I am trying to parameterize Amber force field for a novel molecule, but I couldn't obtain improper dihedrals. Because if I scan impropers like dihedrals; later or sooner the molecule is overlapping ...
2
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0answers
28 views
Generating density matrix of a wavefunction from common quantum chemistry software
I am looking for density matrixes for a couple of closed shell and open-shell systems, and I wonder if there is a trivial way to make e.g. Gaussian just generate an output for me. I may be wrong but ...
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0answers
22 views
How to export .pdb files from PyRx virtual screening? [closed]
I have done a virtual screening with PyRx and I want to visualize the interaction in PyMOL. How can I export PDB files of my macromolecule and my ligand while interacting (binding pose)?
2
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0answers
30 views
Geometry optimisation in Gaussian09
I have looked at various sources regarding this, including the Gaussian official website. However, I have not managed to understand the geometry optimisation method used by Gaussian, a method known as ...
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1answer
39 views
Software for the atom model of all elements [closed]
I want an atom model with shells but I haven't found one yet and the only software that created an atom was Cinema 4D. This software is not for beginners like me and I used a tutorial to make an atom ...
5
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1answer
74 views
Raman spectra in Gaussian [closed]
I want to simulate Raman spectra of benzene in Gaussian 09.
Calculated spectra for a single ring Benzene ($\ce{C6H6}$) in Gaussian differs about $\pu{40 cm^{-1}}$ for each peak, compared with ...
3
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1answer
55 views
Is there a way to check reactions? [closed]
I'm very new to organic chemistry.
I would like to practise simple reactions (HX + Alkenes, X2 with Alkenes and so on) with examples i create myself. Is there a way to check if my products are ...
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1answer
32 views
ChemDraw temporary label for chemnum LaTeX
Currently I'm searching for a nice way to implement my ChemDraw graphics into $\mathrm{\LaTeX}$.
There is a package called chemnum which will auto-label the ...
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0answers
21 views
Software or methods to predict properties of a substance
There's a very similar question here Software for predicting chemical reactions
My question is slightly different. Given a formula for a molecule or a substance consisting of several molecules, is it ...
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1answer
69 views
Molpro - Connection between atomic term symbols and system symmetry
Let's say I have a carbon atom with the electron configuration $1s^22s^22p^2$. We know, that using atomic term symbols we can describe the following states:
$${}^3P_0, {}^3P_1, {}^3P_2, {}^1D_2, {}^...
3
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1answer
43 views
Why is the active space for the dinitrogen cation defined this large in my example?
I have a Molpro script which computes $\ce{N2^+}$ potential energies.
The significant part is the input for the wave function:
...
2
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1answer
45 views
How do I have to interpret the input to the OCC flag in Molpro?
I'm trying to understand the occupied orbital specification in Molpro. They're specified by the OCC flag, while it's stated in the documentation, that
OCC, m1, m2, ..., mn;
where the ...
3
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1answer
57 views
Molpro - Simple explanation of OCC, CORE, FROZEN and CLOSED orbitals
I'm beginning with quantum chemistry and I'm supposed to do some ab initio calculations with Molpro. The problem is, I don't understand the orbital specification very well.
Let's say, I have the ...
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1answer
39 views
How to type condensed formulas in ChemDraw?
What I want is shown in the bubble 1, while what I keep getting every time I change the single bond to a double bond is shown in bubble 2. The H of the middle C in bubble 2 keeps shifting down when I ...
2
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0answers
31 views
Restarting a Gaussian partially constrained relaxed surface scan using GICs
I am Using Gaussian 16 rev D.01, and I want to perform relaxed surface scans where I vary a bond distance. At the same time I constrain seven atom coordinates during the entire optimization (this is ...
2
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1answer
196 views
How to use dispersion correction with TPSSh in Gaussian 16?
A colleague of mine suggested to use TPSSh as a functional. Since I am applying Grimme's D3 dispersion correction by default, I was surprised that it wasn't implemented in the standard density ...
2
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1answer
29 views
Automated Identification of Isomeric Relationship from 3D Structure?
Is there a software package that when given two sets of 3D structures can return the isomeric relationship between them? Even if it was only able to state that they are conformational isomers that ...
4
votes
1answer
88 views
How can I recognize aromatic rings in a connection table?
Given a connection table (that is, a list of atoms, their connectivities/bonds, and the type of bonds), how can I detect the presence of an aromatic ring?
For reference, the aromatic rings in the ...
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0answers
56 views
How to interpret Gaussian output for excited states?
I have calculated the excited energies for benzene in Gaussian. The output therefore was:
...
7
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0answers
142 views
Understanding two-electron integrals in Gaussian 09
I was comparing the two-electron integrals (electron repulsion integrals, ERI) printed by various well-established packages (Gaussian, GAMESS, Molpro etc.) and observed that Gaussian is the oddball in ...
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0answers
17 views
Gas Sensor Simulation
I'm looking for a graphical software to simulate a gas sensor mechanism. I thought "comsol multiphysics" could help me to determine the sensing mechanism of semiconductor gas sensor , but I didn't ...
2
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1answer
39 views
Is there a piece of software that can help me see the (hkl) planes in a crystal lattice?
I am doing research with calcium carbonate structures.
I need a way in which I can familiarize myself with the lattice structure of calcium carbonate polymorphs, especially calcite.
I really struggle ...
1
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1answer
21 views
How to display ligands as ball and stick and macromolecules as cartoons (if protein) / rings (if nucleic acids) in Avogadro?
Avogadro has many good qualities but I can't seem to find a way to display ligands differently to macromolecules in the same view window. Frankly I can't seem to find a way to display any two things ...
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3answers
42 views
How to calculate number of each type of atom in a residue in PyMOL?
I have a 3D model of PDB 4UDC (dexamethasone bound to human glucocorticoid receptor), and I'd like to calculate how many atoms of each element are in the dexamethasone molecule (which has the residue ...
0
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0answers
38 views
How does the “sample type” selection on the MassHunter software for Agilent 7900 ICP-MS affect the quantitative results?
I'm new to using the instrument, and recently I have tried to measure Cr in both the eluent(1% nitric acid) and a method blank (also 1% nitric acid, but after it has gone through the entire analytical ...
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2answers
232 views
How do I make a ZMAT or XYZ file from scratch?
From a structure representation like the one below for Bacteriochlorophyll A, how do I make the ZMAT or XYZ file?
The closest similar question asked here was about converting a PDB entry into XYZ, but ...
3
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0answers
44 views
Chemistry write-ups in LaTex - is it worth drawing figures in LaTex? [closed]
Being an undergraduate chemistry student I have to write a significant amount of hand-ins e.g. lab reports. Up until now I've been using LaTex with mhchem for ...
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1answer
46 views
Is it possible to define the coordinates of an atom using other coordinates while optimizing in gaussian 16?
I know it is possible to fix the value of composite expressions using generalized internal coordinates (gic) in gaussian 16. But is it possible to assign that value to the coordinate of another atom.
...
4
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0answers
136 views
What computational methods are available for predicting nanoparticle structure?
I'm a quantum chemist, and nearly every system I've ever cared about has been studied by DFT. However, I am currently trying to model the surface interactions on a nanoparticle around 100 nm in ...
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votes
1answer
73 views
How to specify complete active spaces in the Dalton software package? [closed]
What do the numbers for specifying the inactive and active space of a Dalton calculation mean?
For example, I do not understand what the following numbers refer to:
...
10
votes
1answer
921 views
How to visualise the total electron density from a Gaussian 16 calculation?
I am trying to generate a 3D visualisation of the total electron density of a molecule. Using Gaussian 16, I have optimised this structure, with DFT, and formatted the resulting ...
1
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1answer
53 views
Library / function for computation of molecular mass / molecular weight in C
We are looking for a function to be used for computing the molecular mass / molecular weight / formula weight in C, either in a library or standalone. So far we have found the following ...
6
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1answer
215 views
Calculating the density matrix from a WFN file
I want to calculate the density for the $\ce{HCN}$ molecule. This molecule has 14 electrons and thus 7 occupied molecular orbitals. I have a .wfn file which ...
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0answers
71 views
Rendering software for publication
Does anyone know how I can render chemical structures of small organic molecules to look like the below images?
I have been looking around, and I cannot seem to find an answer. The closest lead I ...
3
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2answers
379 views
Molpro wavefunction symmetry specification
I'm beginning to use Molpro software for some computations. But I got completely confused by its description of specification of wavefunction symmetry.
It tells us, that the symmetry of wavefunction ...
6
votes
1answer
247 views
What are the preferred IUPAC names of these two compounds?
In a recent homework assignment we are asked to give IUPAC name to the following two compounds:
I am not asking this question for homework help -- for that purpose I got both names correct, to the ...
2
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0answers
40 views
Setting to basis set for electron transfer in type II CdS/TiO2 heterostructre for PYXAID package
I am studying electron injection from $\ce{CdS}$ into $\ce{TiO2}$ using NAMD approach. Now I'm using pyxaid package.
Would be possible someone kindly help me with construction of basis set for this ...
4
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0answers
279 views
Molecular visualization software for Raspberry Pi?
I've been using our lab's code MCMD on my Raspberry Pi for fun and exploratory purposes. I'm trying to find a VMD, Avogadro, Ovito, or other equivalent that is usable on Raspberry Pi, e.g. to view ....
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1answer
64 views
How to unify all the subunits in a PDB file?
A PDB may contain a TER token. For example, hemoglobin has 4 subunits separated by a TER identifier.
If we take hemoglobin's ...
4
votes
2answers
111 views
How to determine if two calibration curves are parallel, within 5%
I have complex matrices and I need to make sure the matrix does not affect the measurement of my analyte. To do that, I need to prepare samples of my analyte in a solvent and of the matrix reinforced ...
2
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0answers
157 views
3D similarity search software [closed]
What software / webservice can one use to find a compound that has similar 3D structure/dimension to another compound?
eg. say we are tying to find a 'better' version of atropine, so naturally we try ...
6
votes
1answer
130 views
How to write an entire trajectory into a single PDB file?
I have a trajectory (few frames) that I want to stack together and build a single PDB. I thought either to use VMD or MDAnalysis library.
With VMD if I do ...
7
votes
1answer
308 views
How do I perform a partial optimisation in GAMESS?
Sometimes it is necessary to perform a partial optimisation of a molecule, i.e. keeping certain variables constant. One example might be to pre-optimise a transition state, taking advantage of not ...
2
votes
1answer
400 views
How to perform a relaxed scan in GAMESS?
I have the following input Gaussian input for my system. The coordinates are given in Cartesian format and it is scanning through 8 steps, with a bond distance between 1 and 5 having a difference of 0....
4
votes
1answer
248 views
How to get force constants in internal coordinates in Gaussian?
I have tried quite a few different ways to get Gaussian to print the force constants in internal coordinates. If the size of the molecule is small then it prints both the internal hessian and ...
4
votes
1answer
216 views
Run a command at every step of a relaxed scan
In Gaussian, I'm trying to do a relaxed scan and for each step obtain the volume. However, when I use the volume keyword, it seems to only output the volume for the initial and final steps. Is there a ...
1
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1answer
106 views
How do I combine z-matrices of multiple molecules into one input stack?
I'd like to run a calculation in Gaussian which requires me to provide cartesian coordinates for reactants and products respectively. My question is how do I combine the cartesian coordinates for two ...
3
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1answer
711 views
How to construct a QST2 input file for Gaussian16 for multiple reactants and products?
I am attempting to determine the transition state structure for the following reaction using the QST2 method on Gaussian 16:
$$\ce{CH3 + N -> HCN + H2 }$$
However, I am struggling to put together ...
3
votes
1answer
228 views
What does the format nF10.8 mean?
I was trying to assign weights to each state in a CASSCF PES scan using nroot=2 in Gaussian. I specified 0.500000 0.500000 at the end of .com file. But it caused the program to assign the weight for ...
1
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1answer
93 views
Generating PDB file from electron density without force field minimization
Is there a step-by-step tutorial on how to generate a PDB file from an electron density file (*.ccp4)?
For my current project, I am trying to take some statistics ...
