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

Neena Susan Eappen neena.susaneappen at mail.utoronto.ca
Fri Nov 2 16:45:48 CET 2018

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

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