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conformer generation
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TUMS

Joined: 15 Mar 2011
Posts: 5

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Link to postPosted: Wed Dec 07, 2011 7:11 amPost subject: conformer generation Reply with quote

Dear chemaxon,

I am using conformers icon in marvin sketch for generating conformers. But now our team want to create conformers by thousonds of molecules. how can we do it?

best,

vpalfi
ChemAxon personnel
Joined: 27 Dec 2010
Posts: 134

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Link to postPosted: Wed Dec 07, 2011 12:47 pmPost subject: Reply with quote

MarvinBeans package contains cxcalx command line program that performs chemical calculations using calculator plugins. The calculations can be performed in single or batch mode.


You can read its documentation here: http://www.chemaxon.com/marvin/help/applications/calc.html
The available calculations are listed in the following page: http://www.chemaxon.com/marvin/help/applications/cxcalc-calculations.html
and a simple example is given for every calculation: e.g.: http://www.chemaxon.com/marvin/help/applications/cxcalc-calculations.html#conformers

For example, if you have an sdf file which contains thousands of molecules and want to calculate the conformers of them, you can run the following command on a command prompt.

C:\>cxcalc -o conformertest.sdf conformers inputmols.sdf


It will result in an output file , conformertest.sdf ,  which contains the conformers of your input molecules - stored in inputmols.sdf.

If you have any further question, please do not hesitate to contact us.

 

Regards,

Viktoria

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