[gmx-users] .top error question

Kai Zhuang kai.zhuang at gmail.com
Thu May 12 19:43:34 CEST 2005

check ur includes again.  
it sounds like u declared 2 default inclusions.  maybe when u added
the includes,
u made an extra copy by accident.  maybe there was the inclusion for
the lipid.itp already before u manually adjusted .bashrc
also, u are using bash right? cuz all the tutorials on gromacs is in
csh.  (i figure u just finished the tutorials since u said u're a
newbie, like me lol)

On 5/12/05, Ramachandra Rao Gullapalli <rrg142 at psu.edu> wrote:
> Dear all,
> Hi i have been trying to grompp on the cluster with the following .top file
> #include "/usr/global/gromacs/share/top/ffgmx.itp"
> #include "/home6/rrg142/gromacs/tieleman-downloads/lipid.itp"
> #include "/home6/rrg142/gromacs/tieleman-downloads/dppc.itp"
> [ system ]
> ; name
> dppc64 lipid in water
> [ molecules ]
> ; name  number
> DPPC    64
> SOL     3846
> And when i run the grompp command, i get an error saying,
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
> checking input for internal consistency...
> calling /lib/cpp...
> processing topology...
> Cleaning up temporary file grompp1L1enX
> Fatal error: Found a second defaults directive, file
> "/home6/rrg142/gromacs/tieleman-downloads/lipid.itp", line 9
> I have included the location /home6/rrg142/gromacs/tieleman-downloads in my
> .bashrc file and yet i am getting this error. What am i missing? I d appreciate
> your advice as im a newbie to both linux and gromacs.
> Is it necessary to include lipid.itp files in the same location as ffgmx.itp?
> Thanks for your time and patience.
> Regards
> Rama
> The important thing is not to stop questioning. Curiosity has its own reason for existing...
> -Einstein
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Kai Zhuang
BioMedical Engineering @ University of Toronto
kai dot zhuang at gmail dot com
kai.zhuang at gmail.com

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