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

[Neena Susan Eappen]

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