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Doubts on minimisation
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Miguel

Joined: 22 Mar 2014
Posts: 7

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Link to postPosted: Tue Apr 21, 2015 11:36 pmPost subject: Doubts on minimisation Reply with quote

Hi!

What would be the best steps to do a minimisation procedure in Marvin 15.2.9 having in mind that I'm preparing ligands for docking? Is it better to use conformers or moldyn?

2nd part of the question: if using moldyn is there anyway to selecrt only the lowest energy conformation from the command line?

 

thank you for your help

Best regards

Miguel

Daniel
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Joined: 22 Jan 2012
Posts: 315

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Link to postPosted: Mon Apr 27, 2015 9:36 amPost subject: Reply with quote

Hi, 

The best solution for your problem would be to use our cxcalc command line tool to generate the lowest energy conformer. You can't select the lowest energy conformer that comes from molecular dynamics.

Use the 

cxcalc leconformer -h

command to get started. 

I hope this helps.

Daniel

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