Re: [AMBER] The parameters for the fully protonated phosphate group

From: David Cerutti <>
Date: Mon, 21 Nov 2016 11:55:32 -0500

> Thanks very much for your reply. As you mentioned, that's exactly the 1-4
electrostatics problem,
> which is ********* as appeared in the output file. So the structure
collapses after several steps of
> minimization. My topology and coordinates have been attached, if you
need. Because the molecule is
> mostly buried in the protein, it is most probably fully protonated,
according to my knowledge. So how
> can I obtain the reasonable parameters for the fully protonated phosphate
group, which can be used to
> perform a stable MD simulation ? Thanks very much !

> Best,
> Jinfeng

Standard prescription is to make a series of deformations of the system,
compute their single point energies, and fit the molecular mechanics basis
functions to reproduce the energy surface. Depending on your system the
molecular mechanics basis functions in Amber may or may not give an
adequate description of the physics. There are a number of options for how
to get the new values of the basis functions: there's ParamFit, FF ParmDev
tied to the RED server, and I've got a program for doing it. Awhile back
there was a guy on here who found my program to do quite well for his
protonated phosphate data, but it was just that--phosphate. Depending on
the size of your molecule you may be in for a bumpier ride.

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Received on Mon Nov 21 2016 - 09:00:04 PST
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