[gmx-users] Opening PDB files in GROMACS on Windows using Cygwin

[Benson Muite]

What version of GROMACS are you using?

On 11/2/18 5:45 PM, Neena Susan Eappen wrote:
> Hello GROMACS users,
>
>
> I am a first time user of GROMACS. According to this excellent tutorial (http://www.mdtutorials.com/gmx/lysozyme/01_pdb2gmx.html), I downloaded the PDB file for lyzozyme, then removed water molecules, typed in the following command on CygwinShell (with GROMACS activated).
>
> $ gmx pdb2gmx -f 1AKI_clean.pdb -o 1AKI_processed.gro -water spce
>
> However, I get an error saying:
>
> In command line option -f, file 1AKI_clean.pdb does not exit or is not accessible.
>
> Please advice where am I going wrong. Any insight would be appreciated.
>
> Many thanks,
>
> Neena Eappen
> Graduate Student
> Jockusch Lab<http://www.chem.utoronto.ca/wp/jockusch/>, U of T