[gmx-users] Help with Error Message
The One And Only
chappyboy29 at gmail.com
Sun Aug 25 03:26:59 CEST 2013
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
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
> > So I started following some tutorials online since I didn't get a
> > 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
> > it asks you to input: pdb2gmx -f protein.pdb -o protein.gro -p
> > -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
> > website at http://www.gromacs.org/Documentation/Errors
> > Help please?
> > --
> > gmx-users mailing list gmx-users at 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-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> gmx-users mailing list gmx-users at gromacs.org
> * 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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
More information about the gromacs.org_gmx-users