[gmx-users] Help with Error Message

[Tsjerk Wassenaar]

Hi ...,

You should have had a look at the topology file format in an earlier step.
At the end is a listing of molecules. As it says in the tutorial, you
replaced solvent by ions, and you have to make changes in the topology file
to match that replacement. Open the file in an editor, have a look around,
try to see where the number of solvent molecules is listed, and make the
changes.

Cheers,

Tsjerk


On Tue, Aug 27, 2013 at 10:41 PM, The One And Only <chappyboy29 at gmail.com>wrote:

> 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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-- 
Tsjerk A. Wassenaar, Ph.D.