[gmx-users] Newbie question

Nataraj B (R&D-Biotech) nataraj at orchidpharma.com
Thu Jan 5 13:21:56 CET 2006

        I am a newbie to GROMACS , I am getting an error while trying to
prepare my protein for MD run at the stage of  "grompp" as per the 
GROMACS flow chart
<http://www.gromacs.org/documentation/reference_3.2/online/flow.html> ) 

The error reported in terminal is 
Fatal error: number of coordinates in coordinate file (out.gro, 378)
             does not match topology (topol.top, 0)
but I checked topol.top file , in which ,of course the coordinates are
differing between out.gro and topol.top, but the error report of  0 as
number of coordinate in topol.top is confusing me.

All the step before grompp, I used everything as default. More I used
spc216.gro (as given in the package) for solvation purpose.  

Please let me know where could possibly I make the mistake. 
More I will be more thankful if any one can provide me the step wise command
to make any protein of your interest for taking it up to setting a
successful dynamics. 

Thanks in advance,

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