On May 20, 2017, at 3:20 PM, P. Buscemi <busce004@umn.edu> wrote:

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

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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

 

<PastedGraphic-1.png>

 

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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