[gmx-users] Problem in Running GROMACS from a different location

David spoel at xray.bmc.uu.se
Thu Nov 13 08:58:01 CET 2003

On Thu, 2003-11-13 at 17:54, Mr.Sridhar wrote:
> Dear GMX users,
> I have some trouble running gromacs.
> Gromacs was originally compiled in one of the users directory
> (TOPOLOGY: /home/bioinfo/jithesh/GROMACS/share/gromacs/top
> BINARIES: /home/bioinfo/jithesh/GROMACS/powerpc-ibm-aix5.1.0.0/power4/bin).
> I have copied the executables and topology directories to my local
> directory (TOPOLOGY: /home/others/SRIDHAR/GROMACS/share/gromacs/top and
> BINARIES: /home/others/SRIDHAR/GROMACS/powerpc-ibm-aix5.1.0.0/power4/bin
> ).
> And I changed the paths in GMXRC,GMXRC.csh,GMXRC.bash files to point to
> my directories.
> And when I run grompp it gave error trying to find topology files
> in the original users directory.
> The log message is............
> ----------------------------------------------------------------
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
> Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
> checking input for internal consistency...
> /home/bioinfo/jithesh/GROMACS/share/gromacs/top: The file access
> permissions do not allow the specified action.

It seems you don't have permission to read the files. ANyway, you can
also set an enviroment variable GMXLIB that points to the correct
XX/share/top directory

> 1cyp_WT.top:11:23: ffG43a1.itp: A file or directory in the path name does
> not exist.
> 1cyp_WT.top:12:20: ions.itp: A file or directory in the path name does not
> exist.
> 1cyp_WT.top:30484:21: posre.itp: A file or directory in the path name does
> not exist.
> 1cyp_WT.top:30491:19: spc.itp: A file or directory in the path name does
> not exist.
> Cleaning up temporary file grompp3KsZEa
> Fatal error: Invalid order for directive moleculetype, file
> ""1cyp_WT.top"", line 14
> -----------------------------------------------------------------
> Is there any way to make the programs run without having to recompile my
> self from the source code.
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David van der Spoel, PhD, Assist. 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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