[gmx-users] Help with Error Message

[The One And Only]

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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>
>