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

[nbhutwal at uci.edu]

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