AMBER Archive (2009)

Subject: Re: [AMBER] phosphorus to carbon on minimization

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Mon Dec 07 2009 - 12:56:28 CST

Dear Alexander,

Here I wonder if the problems your report are not only related to the
graphical program you use to display the output Cartesian
coordinates... For instance, in MM & MD a double bond does not exist;
it is simply represented by a FF constant that is larger than a single
bond. Some graphical programs display a double bond if they detect a
bond below a particular threshold. The color of an atom can be
modified because of a particular name; thus you believe that the
phosphorus atom has turned into a carbon atom but in fact the program
gives a wrong color because of the phosphorus name used...

I might be wrong but I have the strong feeling that this is a problem
of graphical visualization & not a problem related to some "atom
transformation" occurring during the geometry optimization...

regards, Francois

> 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!

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