Re: [O3A] new user

[Paolo T. <pao...@un...>]

Dear John,

the best format to import your file is SDF. qmd stores conformations for 
each molecule in a separate file. You don't need to combine the files. 
The align keyword, if you use candidate=MULTI and specify conf_dir, will 
find the conformational databases for you, provided that you point 
conf_dir to the folder where the conformations are. This step is not 
needed if you invoked the qmd command within the same O3A session (see 
http://open3dalign.sourceforge.net/?Description:Keywords:align).

Cheers,
p.

On 14/05/2016 22:05, John Paul Kowalski wrote:
> Hello, I am a graduate student in Medicinal Chemistry at the 
> University of Washington in Seattle, United States. I have just 
> started to use this software and am very excited for its possibilities 
> as the academic setting in which I am in prevents purchase of 
> commercial software suites that run alignment & QSAR functions. 
> Admittedly, however, I lack any programming experience and my general 
> computer skills are sub-par.
>
> I am emailing to inquire as to whether this discuss list is still 
> active and whether responses will be replied to regarding Open3DAlign 
> & Open3DQSAR or if correspondences should be directed elsewhere?
>
> I may as well post my first software question too -
>
> What is the best file format to use for importing a file with many 
> chemical structures (with or without IC50 values for example) for 
> subsequent energy minimization and alignment? My first attempt of 
> using qmd on a file with many structures yielded individual files for 
> each molecule, or should I recombine these files afterwords?
>
> Thank you,
> John Kowalski
>
>
> ------------------------------------------------------------------------------
> Mobile security can be enabling, not merely restricting. Employees who
> bring their own devices (BYOD) to work are irked by the imposition of MDM
> restrictions. Mobile Device Manager Plus allows you to control only the
> apps on BYO-devices by containerizing them, leaving personal data untouched!
> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
>
>
> _______________________________________________
> Open3dalign-discuss mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/open3dalign-discuss