[gmx-users] Gromacs under Windows
feenstra at chem.vu.nl
Mon Jan 26 09:27:04 CET 2004
Cornel, J. wrote:
> I am running Gromacs under Windows 2000 and am reworking the MD course of RUG with the protein lysozyme. The pdb-file was succesfully converted into aki.top and aki.gro but when I try to generate the tpr-file with grompp I get the following error:
> Back off! I just backed up mdout.mdp to ./#mdout.mdp.5#
> Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
> checking input for internal consistency...
> calling C:\Gromacs\bin\cpp...
> processing topology...
> processing coordinates...
> Fatal error: number of coordinates on coordinate file <aki.gro,1555>
> does not match topology (aki.top,0>
> But I am sure that these numbers are the same 1 protein of 1321 atoms and 78 water molecules (234) is together 1555.
Have you checked your aki.top? Are there lines at the end under the [system]
heading, like this:
protein in water
> I also downloaded the minim.mdp file in the MD course and adapted it to my windows system, at least I think I did. It looks likes this:
> cpp = C:\Gromacs\bin\cpp ; Preprocessor
Are you sure that is the location of your cpp, and that it actually works?
grompp depends on it, but may not always detect a failure...
Try running grompp with the flag '-pp', that will write the cpp pre-processed
topology file. Check at the end if all things still look as you expect them.
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| _ _ ___,| K. Anton Feenstra |
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