[gmx-users] Help with Error Message

The One And Only chappyboy29 at gmail.com
Sun Aug 25 03:40:14 CEST 2013

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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