[Chimera-users] FW: Input from Avogadro, solvation.

P. Buscemi busce004 at umn.edu
Sat May 20 15:20:29 PDT 2017

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 at umn.edu] 
Sent: Saturday, May 20, 2017 5:02 PM
To: chimera-users at 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 ?
Paul Buscemi,
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