Re: [AMBER] phosphorus to carbon on minimization

From: Jason Swails <>
Date: Mon, 7 Dec 2009 13:43:05 -0500


I'm not exactly sure what you mean... The topology file and amber prep files
both have a single phosphorus atom. sander only reads the topology file, it
does not write it, so that phosphorus atom will never change. Why do you
say that it is changing into a carbon?

Moreover, the concept of formal bond order in a topology file is
meaningless. The only properties that bonds have are equilibrium bond
lengths and force constants. The "bond order" would manifest itself in the
values of these variables, as one would expect a shorter equilibrium
distance and stronger force constant for higher-order bonds.

Again, sander will not change any aspects of the topology file, so no atom
mutations or bond properties will change as a result of the simulation.
Both oxygens attached to the phosphorus have the same atom type, so their
bond properties will be identical (I'm not sure if these were the bonds you
were claiming in which one bond took on double-bond properties?), but their
equilibrium lengths and bond strengths will be the same (as would be
expected for nearly equivalent oxygens). The minimization will push all
bonds towards their equilibrium values, so if a bond is becoming shorter,
that's because the stored bond-length for those atom types are similar to a
"double-bond" bond length.

My guess is that you may be mis-interpreting some of the output files, since
no visualization program that works with amber files would change a P to a
C. If this missed the point of your question, then perhaps you can be a
little more descriptive and provide some of the sander output files?

Good luck!

On Mon, Dec 7, 2009 at 10:48 AM, Alexander Boncheff <>wrote:

> 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
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Mon Dec 07 2009 - 11:00:02 PST
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