I found that the daily update 2017 05 16 could not open Avogadro files, but that stable version 1.11.2 could. Hope this helps you. Paul From: P. Buscemi [mailto:busce004@umn.edu] Sent: Saturday, May 20, 2017 5:20 PM To: 'BB' Subject: FW: Input from Avogadro, solvation. Dear Chimera, This is the other common error which strangely appears to occur on my PC much more frequently than on my iMac – using the same mol2 file From: Paul Buscemi [mailto:busce004@umn.edu] Sent: Saturday, May 20, 2017 5:02 PM To: chimera-users@cgl.ucsf.edu BB Subject: Input from Avogadro, solvation. Dear Chimera, Three basic questions: I’m using Avogadro to construct my models and import as mol2 or pdb types. I often obtain messages as or that the atom is not “listed” . Is there a preparation I can use for transfer of models ? Alternatively do you suggest any other program to construct models ? 2) If I use Tools to solvate a model, should I use the “Start solvate tool” under MD and/or check “Periodic Boundary Conditions. 3) Im considering building a multicore system ( two 16 core Xeon’s) as a 64 bit system would Chimera take advantage of the multi-core system ? Would the upgrade funds be better spent on memory ? Regards, Paul Buscemi, UMN BICB
