[Chimera-users] Input from Avogadro, solvation.

[Paul Buscemi]

Thanks you Elaine,

This was quite helpful.  I read a response from Eric who addressed the first question.  It was a bug in a daily build but now fixed.

I did re-ask #2 and 3  because I read his response first.    Yes I use min and MD  and yes, for me the box is a necessity.

Best
Paul
> On May 22, 2017, at 3:54 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Paul,
> (1) It is generally impossible to figure out what is going on without having examples of your file(s) and being able to reproduce the problem.  I’ve never used Avogadro or files from Avogadro.  Make sure the PDB or mol2 file is plain text, but that might not be the problem.   You could try using menu: Help… Report a Bug and include a brief description of what you did and attach an example file.   
> 
> (2) You didn’t say, but I’m guessing you are using Minimize Structure and/or Molecular Dynamics. If you already used the Solvate tool, there is no need to click the button on the Molecular Dynamics tool to open the Solvate tool again.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html
> 
> I don’t know if you want your molecular dynamics calculation to use periodic boundary conditions or not.  You need to figure that out and then set the option accordingly.  If you do choose that option, you need to have added a solvent box.
> 
> Others will have to weigh in about your other issues since I don’t know the answers.  Best,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
>> On May 20, 2017, at 3:02 PM, Paul Buscemi <busce004 at umn.edu> wrote:
>> 
>> 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