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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.Thank you, Neena
Neena1490
Posted 2018-11-02T15:08:01.007
Reputation: 11
where is the file 1AKI_clean.pdb ? – matzeri – 2018-11-02T17:44:30.703
Thank you for pointing that out, now that I transferred the file into working directory, I do not get that error anymore. – Neena1490 – 2018-11-03T02:09:39.703