[gmx-developers] One more correction for Amber FF

Igor Leontyev ileontyev at ucdavis.edu
Sun Apr 17 01:58:37 CEST 2011

>>>> 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 

More information about the gromacs.org_gmx-developers mailing list