[gmx-developers] One more correction for Amber FF
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
>>>> 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
>> parameters in the original Amber program. Suggested correction in
>> ;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
> 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.
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