[gmx-users] Help with Error Message

[The One And Only]

that's something i know nothing about; I just graduated from high school
and I have no background or experience in open source projects or programs
like pymol/gromacs. My professor wants me to be able to produce a setup,
simulation, and analysis within a week so I'm pretty desperate right now in
terms of getting help. Do you know how to get the right .pdb file in my
working directory?


On Sat, Aug 24, 2013 at 6:23 PM, Rafael I. Silverman y de la Vega <
rsilverm at ucsc.edu> wrote:

> 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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