It sounds like you dont have the .pdb file in your working directory. Perhaps you need to learn a bit about unix filesystems
On Sat, Aug 24, 2013 at 6:18 PM, The One And Only <chappybo...@gmail.com>wrote: > So I started following some tutorials online since I didn't get a response > last time. the tutorial I'm using is: > http://nmr.chem.uu.nl/%7Etsjerk/course/molmod/ > I followed that tutorial to the second page and got stuck at the step where > it asks you to input: pdb2gmx -f protein.pdb -o protein.gro -p protein.top > -ignh > I picked GROMOS96 45a3 force field(11) for the force field and spc(1) for > the water model but got the following error message: > Opening force field file > /usr/local/gromacs/share/gromacs/top/gromos45a3.ff/aminoacids.r2b > Reading protein.pdb... > > ------------------------------------------------------- > Program pdb2gmx, VERSION 4.6.3 > Source code file: > /Users/christinalin/wget-1.14/gromacs-4.6.3/src/gmxlib/futil.c, line: 593 > > File input/output error: > protein.pdb > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > > Help please? > -- > 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 > -- 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