[gmx-users] File input/output error pdb2gmx command

[Justin A. Lemkul]

nbhutwal at uci.edu wrote:
> Hello.
> 
> In GROMACS, within a terminal window on linux ubuntu, I am having trouble
> with a pdb2gmx command. The file I am trying to convert to a gmx file is
> called 1OTI.pdb. I type in pdb2gmx -f 1OTI.pdb -o 1OTI_processed.gro
> -water spce and hit enter. When it prompts me for a forcefield, I enter
> the no. corresponding to the forcefield I want, but get a file input
> output error: Specifically:
> 
> File input/output error:
> 1OTI.pdb
> 
> My initial guess was that it cannot find the file. However, I typed in the
> command "pwd" into the terminal and got back /home/nbhutwal. I opened this
> directory from my desktop and found that that is where I saved the file
> 1OTI.pdb, confusing me even more haha. Could someone maybe shed some more
> light on this error. Much appreciated!
> 

Confirm that the file is in the working directory with 'ls' and you'll know for 
sure.  The home directory and desktop are different directories.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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