[gmx-users] Help with Error Message

[The One And Only]

I've moved on from that point; now I'm stuck at where it asks me to remove
molecules of solvent from the topology file.


On Tue, Aug 27, 2013 at 1:33 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> 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.
> --
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