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

[Dallas Warren]

Though this looked familiar:

http://lists.gromacs.org/pipermail/gmx-users/2011-November/066557.html

What are the permissions for the file?

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail. 

> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] On Behalf Of nbhutwal at uci.edu
> Sent: Tuesday, 6 December 2011 10:56 AM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] File input/output error pdb2gmx command
> 
> 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!
> 
> -Neil
> 
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