[gmx-users] Need Help
spoel at xray.bmc.uu.se
Thu Jul 28 21:02:29 CEST 2005
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
> 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
> cpp exit code: 33
> Tried to execute: 'c:\Progra~1\Gromacs\bin\cpp -I C:\Progra~1\Gromacs
> -I D:\Gromacs\share\top -IC:\Program Files\Gromacs\share\top
> topol.top > grompp
> 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,
> does not match topology (topol.top, 0)
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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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