[gmx-users] File input/output error: 1OTI.pdb

Mark Abraham Mark.Abraham at anu.edu.au
Tue Nov 29 06:38:50 CET 2011

On 29/11/2011 4:10 PM, nbhutwal at uci.edu wrote:
> Hello all. I have just started research and will be using Gromacs. I am
> not very command prompt or linux or programming savvy and I'm slowly
> learning how to do certain things. I was trying to convert a pdb file
> using pdb2gmx but keep getting the following error:
> "File input/output error: 1OTI.pdb".
> I'm not entirely sure how to solve this issue. The command I wrote is as
> follows:
> pdb2gmx -f 1OTI.pdb -o 1OTI_processed.gro -water spce
> I am going through the lysozyme tutorial I found for gromacs. Any help
> would be greatly appreciated! Thank you!

Something is wrong with that file, like inappropriate read/write 
permissions on it or the directory in which you are trying to work. The 
latter should be a subdirectory of your home directory. Do consider 
doing general linux tutorial material to acquire experience, if appropriate.


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