Good Afternoon I am using the first version of Avagadro. I am trying to optimize geometry while preserving certain angles. I know it is possible to constrain specific positions, or to ignore certain atoms entirely.
When I go to Extensions-> Molecular Mechanics-> Constraints... menu, I specify torsional angle, then input the specified angle and atomic indices. The index choices allow only numeric input, so I am not sure how the program differs between, for example, C1 or H1, for an input of 1. I assume it might consider spacial arrangements and then locate the closest atom compared to other indices prescribed. When then selecting UFF (or any force field), the relaxation does not constrain the specified requirements. Moreover, when going to View->Properties->Torsion Properties..., I set the angles as close to desired angle as possible (changing one angle affects another). This still does not force the set constraints to hold. When using other constraints like fix atom, the application works, but has severe consequences in molecular geometry producing chemically false geometries. Could you please provide me with a process to either a.) keep a specific symmetry of a molecule constant or b.) set torsional angles to specific quantity and keep them constant without constraining the atoms specific position. Thanks -- Thanks for your time, Gregory Theophall Rensselaer Polytechnic Institute 110 8th St Troy, NY 12180 ------------------------------------------------------------------------------ Monitor 25 network devices or servers for free with OpManager! OpManager is web-based network management software that monitors network devices and physical & virtual servers, alerts via email & sms for fault. Monitor 25 devices for free with no restriction. Download now http://ad.doubleclick.net/ddm/clk/292181274;119417398;o _______________________________________________ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
