[gmx-users] Did not find any molecules of type ...

[Mark Abraham]

Hi,

That means there's two definitions of a WAT [moleculetype]. You need to
find both in your set of #included files, and work out where the error lies.

Mark

On Mon, Feb 22, 2016 at 1:55 PM Marta Wisniewska <
marta.d.wisniewska at gmail.com> wrote:

> Hello Justin,
>
> my topology file:
>  WAT_GMX.top created by acpypi on Tue Mar  3 13:26:34 2009
>
> ; Include forcefield parameters
> #include "amber99sb-star-ildnp.ff/forcefield.itp"
>
> [ moleculetype ]
> ;molname          nrexcl
> WAT             2
>
> [ atoms ]
> ; id  at type     res nr  res name   at name  cg nr  charge    mass
>   1   O           1       WAT        O       1      -0.834    16.00000
>   2   H           1       WAT        H1      1       0.417     1.00800
>   3   H           1       WAT        H2      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
>
>
> ; Include water topology
> #include "amber99sb-star-ildnp.ff/tip3p.itp"
>
> [ system ]
> WAT in water
>
> [ molecules ]
> ; Compound       #mols
> WAT              1
> SOL              1023
>
>
> I have olny one molecule (exactly it is a water molecule. tip3p model).
>
> If I put into topology file:
> #include "./wat.itp"
>
> I get a new error, such as : moleculetype WAT is redefined.
>
> How to fix it?
>
> Thank you in advance!
>