Search found 79 matches
- Thu Feb 16, 2023 12:16 am
- Forum: Computational Chemistry Exercises
- Topic: Viewing electrostatic potential and dipole moment vector
- Replies: 5
- Views: 70251
Re: Viewing electrostatic potential and dipole moment vector
An updated version of a "dipole+esp surface" display in Jmol and Jsmol is given at the following URL: https://tinyurl.com/2vsksdbp . This example uses a less-symmetric molecule otimized in ORCA. In the example given above, the water dipole moment just happens to align with the default dipole produce...
- Sat Feb 11, 2023 7:49 am
- Forum: Computational Chemistry Exercises
- Topic: Viewing electrostatic potential and dipole moment vector
- Replies: 5
- Views: 70251
Re: Viewing electrostatic potential and dipole moment vector
Hi Mark, Jmol can display various surfaces, molecules, and graphic items simultaneously. First you need to do a Molecular Orbital calculation in WebMO. Do File, Export molecule as .mol. Display the electron density, and do File, Export Molecule, as .cub. Then display the electrostatic potential, and...
- Wed Nov 30, 2022 9:46 pm
- Forum: WebMO 22
- Topic: Errror reading charge in a .mol file
- Replies: 6
- Views: 10583
Re: Errror reading charge in a .mol file
Avogadro 1.2 and 1.97 both put a +3 charge on S when opening the above .mol file. OpenBabel 3.1.1 converts this SO2.mol file into Sybyl-mol2 format as follows: @<TRIPOS>MOLECULE ***** 3 2 0 0 0 SMALL GASTEIGER @<TRIPOS>ATOM 1 S -1.0184 1.3212 -23.9010 S.3 1 UNL1 0.1816 2 O 0.7228 1.4965 -23.9010 O.3...
- Mon Nov 21, 2022 7:32 pm
- Forum: WebMO 22
- Topic: Errror reading charge in a .mol file
- Replies: 6
- Views: 10583
Re: Errror reading charge in a .mol file
See the following web page for the formatted SO2 .mol test:
https://chem4.cns.uaf.edu/webmo1/so2-formatted-mol.htm
https://chem4.cns.uaf.edu/webmo1/so2-formatted-mol.htm
- Mon Nov 21, 2022 6:19 pm
- Forum: WebMO 22
- Topic: Errror reading charge in a .mol file
- Replies: 6
- Views: 10583
Re: Errror reading charge in a .mol file
More: After assigning charges, do Cleanup, Comprehensive-Idealized. The .mol text in the above window was modified by the Forum program so that it cannot be imported. To test my assertion, one would therefore need to rebuild SO2 per the directions given. Note that crucially the .mol file does record...
- Mon Nov 21, 2022 5:57 pm
- Forum: WebMO 22
- Topic: Errror reading charge in a .mol file
- Replies: 6
- Views: 10583
Re: Errror reading charge in a .mol file
(1) Build SO2 with 1 db and 1 sb. Add charges by right-clicking S (+1) and one O (-1). Then File, Export Molecule as mol/sdf format, creating a "molecule.mol" file in the download folder. (2) Now start over: File, New. File, Import Molecule as mol/sdf, Choose File, find the above molecule.mol file, ...
- Sun Nov 20, 2022 8:17 pm
- Forum: WebMO 22
- Topic: Errror reading charge in a .mol file
- Replies: 6
- Views: 10583
Errror reading charge in a .mol file
WebMO v. 22 (demo site) and v. 19 (local) insert +3 charge on S when importing a .mol file. Try this .mol file, which was exported from WebMO in mol/sdf format: ---------------------- WebMO 3 2 0 0 1 V2000 0.0000 0.6833 0.0000 S 0 1 0 0 0 0 0 0 0 0 0 0 -0.5726 -0.6896 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 ...
- Wed Oct 12, 2022 6:50 am
- Forum: WebMO Installation on Linux
- Topic: Install WebMO 22 on ubuntu 22.04
- Replies: 2
- Views: 13558
Re: Install WebMO 22 on ubuntu 22.04
Eancedeg-Its not clear what your goal is here. Do you want one server box to host WebMO and compute engines, and also serve regular web pages out of /var/www? If so, one can just install an Oracle VirtualBox VM on the Linux/WebMO machine, then install Ubuntu (or the distro of your choice) on the VM ...
- Mon Sep 05, 2022 8:41 pm
- Forum: WebMO Installation on Linux
- Topic: Rocky Linux 9 and OpenMopac
- Replies: 0
- Views: 35564
Rocky Linux 9 and OpenMopac
I was disappointed that the effective EOL of CentOS 8 came so soon, so I was glad to discover that Rocky Linux, now at v 9, is a good replacement. I have installed WebMO 22, G16, and ORCA 5 by just following the directions on this site. The installation script for OpenMopac (openmopac-x.x.x-linux.ru...
- Mon Sep 05, 2022 8:29 pm
- Forum: Other
- Topic: MOPAC v 22 EPEL package
- Replies: 0
- Views: 33855
MOPAC v 22 EPEL package
Dr. Susi Lehtola has installed a RHEL 9 package for MOPAC 22 in the EPEL repository. If you have enabled EPEL on your system, all you need to do, as root, is # dnf install mopac The mopac executable and parameter file are installed in /usr/bin. Therefore in the Interface Manager one should enter the...