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

[P. Buscemi]

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 at 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 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 ?
 
Regards,
 
Paul Buscemi,
UMN BICB
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