[gmx-users] Need Help

[David]

On Thu, 2005-07-28 at 16:38 +0100, Ur-Rehman, Saif wrote:
> I am trying to run a simulated annaeling simulation on a 6 residue
> peptide which i chopped out of beta lactoglobulin.
> I am using Windows and  grommpp  absolutely refuses to work. I have
> read a previous posting that this error is down to the path for the
> cpp not being set right in the mdp file. However no matter how i
> change the path it results in this error
> I think it might have to do with the fact that theres a space in the
> path. however i cannot reinstall it as i do not have the privileges on
> the network to do so. Is there a way round this kind of situation
>  
> Thanking you in advance
>  
> Saif
>  
> grompp.mdp has this in it at the moment
> 
> title = Beta-Lac
> 
> cpp = c:\Progra~1\Gromacs\bin\cpp 
> 

Is cpp really there?
In that case try to use double backslashes...

> include = -I C:\Progra~1\Gromacs\share\top 
> 
> 
>  
> and running grompp results in
>  
> calling c:\Progra~1\Gromacs\bin\cpp...
> \Progra~1\Gromacs\bin\cpp: Files\Gromacs\share\top: No such file or
> directory
> cpp exit code: 33
> Tried to execute: 'c:\Progra~1\Gromacs\bin\cpp -I C:\Progra~1\Gromacs
> \share\top
> -I D:\Gromacs\share\top -IC:\Program Files\Gromacs\share\top
> topol.top > grompp
> a01720'
> The 'c:\Progra~1\Gromacs\bin\cpp' command is defined in the .mdp file
> processing topology...
> processing coordinates...
> Fatal error: number of coordinates in coordinate file (conf.gro,
> 23727)
>              does not match topology (topol.top, 0)
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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