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 [email protected] +61 3 9903 9304 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. > -----Original Message----- > From: [email protected] [mailto:gmx-users- > [email protected]] On Behalf Of [email protected] > Sent: Tuesday, 6 December 2011 10:56 AM > To: [email protected] > 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 > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
