nbhut...@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
--
========================================
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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