AMBER Archive (2009)

Subject: [AMBER] phosphorus to carbon on minimization

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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: a.top

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• Previous message: Piotr Cieplak: "[AMBER] force field parameters"
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• Reply: Jason Swails: "Re: [AMBER] phosphorus to carbon on minimization"
• Reply: FyD: "Re: [AMBER] phosphorus to carbon on minimization"
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