[gmx-developers] One more correction for Amber FF

Shirts, Michael (mrs5pt) mrs5pt at eservices.virginia.edu
Sun Apr 17 03:03:10 CEST 2011

So in other words, Amber isn't actually using TIP3P, then.  So the question
is, does one use AMBER, or does one use TIP3P.  This is actually a pretty
hard call.  And actually, sounds like something the AMBER people should be
changing.  I don't know a good solution.

Another question is, what's the practical difference?  I might actually take
a look at this. . .

Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu

> From: Igor Leontyev <ileontyev at ucdavis.edu>
> Reply-To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Date: Sat, 16 Apr 2011 19:58:37 -0400
> To: "gmx-developers at gromacs.org" <gmx-developers at gromacs.org>
> Subject: [gmx-developers] One more correction for Amber FF
>>>>> On 2011-04-15 23.06, Igor Leontyev wrote:
>>>>> Current vdW parameters of Amber TIP3P water (OW atom) are slightly
>>>>> different from those in Sorin's Amber port: "3.15076e-01 6.35968e-01".
>>>>> Later are in excellent agreement with the original amber TIP3P
>>>>> parameters:
>>>>> R*=1.7683 A and Eps= 0.1520 Kcal/mol.
>>>> Sorry but can you be more specific? Is there a new parameterization of
>>>> TIP3P in Amber? For which force fields?
>>> OW parameters in gromacs port of amber (all versions 94-03) differ from
>>> the
>>> parameters in the original Amber program. Suggested correction in
>>> amberXX.ff/ffnonbonded.itp:
>>> ;OW           8      16.00    0.0000  A   3.15061e-01  6.36386e-01
>>> OW           8      16.00    0.0000  A   3.15076e-01  6.35968e-01
>> Have you tried to email Eric Sorin (cc'ed in this email) to ask about
>> this?
>> I suspect he could explain better.
> As I understand, the slight difference appeared due to rounding. TIP3P
> parameters in port of  Eric Sorin are taken from the paper Mahoney &
> Jorgensen (2000). J. Chem. Phys. 112, 8910-8922, where the parameters are:
> sigma=3.15061 A, eps=0.1521 kcal/mol.
> While the parameters in original Amber parm99.dat file are
> R*=1.7683 A (i.e. sigma=3.15075) eps=0.1520 kcal/mol.
> Thus, to achieve an exact correspondence of forces and energies obtained
> with Gromacs and Amber codes we need to use the original amber parameters,
> as suggested above.
> Igor Leontyev 
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