VConf![]() |
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VConfVConf is a programme that is useful for a preliminary investigation into the conformations of a molecule. It is not very accurate, but for a very flexible molecule can give you a more comprehensive idea of where to start than a search of the CSD would. Obviously, all potential minima should be investigated further with GAUSSIAN. It was written as a conformational search program for ligands, and was recommended to Sally by Prof Chai-en A Chang, University California Riverside, (chianenc@ucr.edu) during her visit to the US in July 2012. It is licensed to the group for research until Aug 2013, (see license.txt). The full user manual is available at http://www.verachem.com/vconf_v2.pdf The input fileThe input file is in .sdf format. This can be saved from Mercury (File > Save As > MOL files (*.mol, *.sdf, *.sd, *.mdl) > change the file extension to .sdf). If you save as .mol and rename later to .sdf you get a different format. The format of this needs editing a bit to work with VConf, as described in this file. The first section describes the origin of the input file (usually a CCDC deposition). The second section describes the atoms. The third section describes the bonds. AtomsFor each atom you have the following information
To get you started, just copy the following to after your element label (which is I have assumed is 1 character long so ensure you remove one of the leading spaces if you have a 2 character element label). You WILL be overwriting a number if you are working with Mercury output, and this is the charge on the atom. 0 0 0 0 0 0 0 0 0 0 0 0 Change any charges or chiralities if you want. BondsFor each bond you have the following information
To get you started, just copy the following to after your bond order 0 0 0 0 According to Sally's notes, aromatic bonds are not accepted, so change any aromatic rings to alternate between single and double bonds. This has not been tested by Louise Running VConfVConf in installed on blackadder and can be run using the command
There are a number of options that can be changed in the run.
The output filesThere is a .log file that tells you The *_vconf.sdf file is the lowest energy conformation found in the search. The *_confs.sdf file lists all the conformations in order of energy. It is very useful to edit this in vi first to change the names of the molecules. The $$$$ line separates each conformation, and the following line is the title of the molecule, which is visible in Molden. The VConf output has these all with the same name. | |||||||||
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