[gmx-users] Can you help me ?

[Yang Ye]

Try put Cl- under [ molecules ]

job560 at sohu.com wrote:
>
> when I use the following command ,there always a error message.Can you
> help me ? Thank you very much !
>
> command: grompp -f em.mdp -c trp_b4em.gro -p trp.top -o trp_em.tpr
>
> error message:
> .
> .
> creating statusfile for 1 node...
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
> checking input for internal consistency...
> calling /usr/bin/cpp...
> processing topology...
> Generated 279 of the 1225 non-bonded parameter combinations
> Excluding 3 bonded neighbours for Protein 1
> Excluding 3 bonded neighbours for IN4 1
> Excluding 2 bonded neighbours for SOL 4145
> Cleaning up temporary file gromppD2IkOr
> -------------------------------------------------------
> Program grompp, VERSION 3.3
> Source code file: toppush.c, line: 1264
> Fatal error:
> No such moleculetype Cl
> -------------------------------------------------------
>
> enviroment:
>
>
> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++=
+++++++++++++++++++++++++++
> extra information:
> OS: Red Hat Linux AS4
> fftw: fftw-3.1.2.tar.tar
> gromacs: gromacs-3.3.tar.gz
>
> installation :
> 1.fftw
> ./configure --enable-float
> make
> make install
> 2. gromacs
> ./configure CPPFLAGS=3D"-I/gromacs/gromacs-3.3/include"
> LDFLAGS=3D"-L/gromacs/fftw-3.1.2/libbench2"
> make
> make install
> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++=
+++++++++++++++++++++++++++
>
>
>
> -----------------------------------------------------------------------=
-
> *=D3=C3=CB=D1=B9=B7=C6=B4=D2=F4=D0=B4=D3=CA=BC=FE=A3=AC=CC=E5=D1=E9=B8=FC=
=C1=F7=B3=A9=B5=C4=D6=D0=CE=C4=CA=E4=C8=EB>>
> <http://goto.mail.sohu.com/goto.php3?code=3Dmailadt-ta>
>
> -----------------------------------------------------------------------=
-
>
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