AMBER Archive (2009)

Subject: [AMBER] phosphorus to carbon on minimization

From: Alexander Boncheff (
Date: Mon Dec 07 2009 - 09:48:45 CST

Hi guys,

I'm not sure how this happens but I have a molecule with a phosphorus functional group. Whenever I do the sander minimization the phosphorus gets turned into a carbon and some of the bonds connecting to the phosphorus get changed (single bonds to double bonds). I've attached the .prep file and the resulting .crd and .top files. Thanks for any advice anyone can give!

- Alex Boncheff

  • application/octet-stream attachment: a.prep

  • application/octet-stream attachment: a.crd

  • application/octet-stream attachment:

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