WebMO Support Forum

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...

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...

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...

See the following web page for the formatted SO2 .mol test:

https://chem4.cns.uaf.edu/webmo1/so2-formatted-mol.htm

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...

(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, ...

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 ...

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 ...

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...

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...