[gmx-users] acpype generated different tip3p water paramters

[Alan]

Hi Yun,

ACPYPE is working fine. What happens here is I choose the reproduce the
exact values one sees in AMBER.

Now why GMX tip3p file choose a different value, I don't know.

Nevertheless, it's pretty simple to put whatever value you want there if you
think you need.

Alan

On 26 September 2011 17:35, Yun Shi <yunshi09 at gmail.com> wrote:

> Hi all,
>
> I just noted that the tip3p water converted from amber format to gromacs
> format is
>
> [ moleculetype ]
> ; molname       nrexcl ; TIP3P model
>   WAT             2
>
> [ atoms ]
> ;   nr   type  resnr residue  atom   cgnr     charge       mass
>      1     OW      1     WAT     O      1     -0.834   16.00000
>      2     HW      1     WAT    H1      1      0.417    1.00800
>      3     HW      1     WAT    H2      1      0.417    1.00800
>
> #ifdef FLEXIBLE
> [ bonds ]
> ; i j   funct   length  force.c.
> 1   2   1   0.09572   462750.4 0.09572   462750.4
> 1   3   1   0.09572   462750.4 0.09572   462750.4
>
> [ angles ]
> ; i j   k   funct   angle   force.c.
> 2   1   3   1   104.520    836.800  104.520    836.800
> #else
> [ settles ]
> ; i j   funct   length
> 1   1   0.09572 0.15139
>
> [ exclusions ]
> 1   2   3
> 2   1   3
> 3   1   2
> #endif
>
>
> while in amber99sb.ff/tip3p.itp. it is
>
>  moleculetype ]
> ; molname       nrexcl
> SOL             2
>
> [ atoms ]
> ; id  at type     res nr  res name  at name  cg nr  charge    mass
>   1   OW          1       SOL       OW       1      -0.834    16.00000
>   2   HW          1       SOL       HW1      1       0.417     1.00800
>   3   HW          1       SOL       HW2      1       0.417     1.00800
>
> #ifndef FLEXIBLE
>
> [ settles ]
> ; OW    funct   doh     dhh
> 1       1       0.09572 0.15139
>
> [ exclusions ]
> 1       2       3
> 2       1       3
> 3       1       2
>
> #else
>
> [ bonds ]
> ; i     j       funct   length  force_constant
> 1       2       1       0.09572 502416.0   0.09572        502416.0
> 1       3       1       0.09572 502416.0   0.09572        502416.0
>
>
> [ angles ]
> ; i     j       k       funct   angle   force_constant
> 2       1       3       1       104.52  628.02      104.52  628.02
>
> #endif
>
> So it seems that the force_constants for O-H bond and H-O-H angle are
> different? Does this mean amber and gromacs use different parameters for
> tip3p water? or it's just acpype is not working right?
>
> Thanks,
> Yun
>
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-- 
Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt - PANDA, EMBL-EBI
CB10 1SD, Hinxton, Cambridge, UK
+44 1223 49 4588
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