[gmx-users] number of coordinates in coordinate file

[Mark Abraham]

> Dear all,
> I am trying to do Energy Minimization of a protein.But it gives the
> following error:
> ERROR: invalid enum 'cut-��off' for variable vdw-type, using
> 'Cut-off'
> Next time use one of: 'Cut-off' 'Switch' 'Shift' 'User' 'Encad-shift'

I expect you've written your .mdp file using something other than an
editor that writes plain text. Use an editor that writes plain text, and
ensure that you have unix-style line endings (using dos2unix if needed).
Using a (for examlpe) Windows desktop for computational chemistry on a
unix platform requires care and attention to these details.

> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
> checking input for internal consistency...
> calling /usr/bin/cpp �� the c
> pre��processor...
> cpp: too many input files
> cpp exit code: 256
> Tried to execute: '/usr/bin/cpp �� the c
> pre��processor -I/usr/share/gromacs/top
> -I/usr/share/gromacs/top ��-DPOSRES_SPC 2a5f.top >
> gromppGMSvC5'
> The '/usr/bin/cpp �� the c pre��processor'
> command is defined in the .mdp file
> processing topology...
> processing coordinates...
> -------------------------------------------------------
> Program grompp, VERSION 3.3.1
> Source code file: grompp.c, line: 448
>
> Fatal error:
> number of coordinates in coordinate file (2a5f_b4ion.gro, 23644)
>              does not match topology (2a5f.top, 0)
> What Should I do and how can I remove the input files, as mentioned above
> that
> cpp: too many input files.

See
http://wiki.gromacs.org/index.php/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology

Mark