[gmx-users] Opening PDB files in GROMACS on Windows using Cygwin
Bratin Kumar Das
177cy500.bratin at nitk.edu.in
Fri Nov 2 16:51:44 CET 2018
What ever version you use if the file is not present in your working
..it will give the same error
On Fri, Nov 2, 2018, 9:18 PM Benson Muite <benson.muite at ut.ee> wrote:
> 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
> > 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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