[gmx-users] Help with Error Message

Rafael I. Silverman y de la Vega rsilverm at ucsc.edu
Sun Aug 25 03:23:41 CEST 2013

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 <chappyboy29 at 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?
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