[gmx-users] Help with Error Message

[Tsjerk Wassenaar]

Hey :)

Sorry for replying a bit late. But the issues you mention in this and the
other posts are usually solved by closely reading the text of the tutorial,
not only the commands.

Cheers,

Tsjerk


On Sun, Aug 25, 2013 at 3:44 AM, The One And Only <chappyboy29 at gmail.com>wrote:

> Never mind, I'm dumb. I just realized that protein.pdb means i have to
> specify which protein i want like "1qlz.pdb" and not actually type
> "protein.pdb" BUT THANKS GUYS!!
>
>
> On Sat, Aug 24, 2013 at 6:40 PM, The One And Only <chappyboy29 at gmail.com
> >wrote:
>
> > so how do i solve the protein.pdb issue?
> >
> >
> > On Sat, Aug 24, 2013 at 6:37 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >>
> >>
> >> On 8/24/13 9:26 PM, The One And Only wrote:
> >>
> >>> 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?
> >>>
> >>>
> >> Rudimentary Unix commands like cp and mv are covered in any Unix/Linux
> >> tutorial.  Google can find lots of good ones.  Producing a quality
> >> simulation cannot be rushed, and if you don't know the fundamentals of
> >> navigating the command line and directory structure, it's nearly
> >> impossible.  You need to invest time in learning the environment before
> >> doing anything, I'm afraid.  Just to give a bit of perspective, we used
> to
> >> train our undergrads for nearly a full semester (at least 2-3 months)
> >> before requiring them to do any "real" work.  At least a week or two of
> >> that time was spent getting used to command line and Linux in general.
> >>
> >> -Justin
> >>
> >> --
> >> ==============================**====================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Postdoctoral Fellow
> >>
> >> Department of Pharmaceutical Sciences
> >> School of Pharmacy
> >> Health Sciences Facility II, Room 601
> >> University of Maryland, Baltimore
> >> 20 Penn St.
> >> Baltimore, MD 21201
> >>
> >> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu>|
> (410)
> >> 706-7441
> >>
> >> ==============================**====================
> >> --
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-- 
Tsjerk A. Wassenaar, Ph.D.