[Chimera-users] Input from Avogadro, solvation.

Paul Buscemi busce004 at umn.edu
Mon May 22 18:09:34 PDT 2017


Thanks for the response,

A redownload worked...

would you please take a stab at  particularly #2 .   For # 3  I saw an 2013 blog that multicore was not supported and I take this to still be the case.

Regards,
Paul


> On May 22, 2017, at 4:48 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> 
> This particular bug was fixed on the 19th — if you get the current daily build you won’t get this “coercing to Unicode” error.
> 
> —Eric
> 
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab
> 
>>  
>> From: Paul Buscemi [mailto:busce004 at umn.edu <mailto:busce004 at umn.edu>] 
>> Sent: Saturday, May 20, 2017 5:02 PM
>> To: chimera-users at cgl.ucsf.edu <mailto: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
>>  
>> <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 > Amber> solvate to solvate a model,  should I use the “Start solvate tool” under  when starting a MD run  ?  

>>  
>>  
>> 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  or just a great CUDA GPU ?
>>  
>> Regards,
>>  
>> Paul Buscemi,
>> UMN BICB
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