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 gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
