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 chappybo...@gmail.comwrote:
Never mind, I'm
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 tsje...@gmail.com wrote:
Hey :)
Sorry for replying a bit late. But the issues you mention in this and the
other posts are
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
What kind of editor should I open it in? I have Pymol, but I don't know if
it's the right one.
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a text editor
On Tue, Aug 27, 2013 at 1:54 PM, The One And Only chappybo...@gmail.comwrote:
What kind of editor should I open it in? I have Pymol, but I don't know if
it's the right one.
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An editor is a program to edit the text in a file: gedit, nano, vi, emacs,
... It'll be the equivalent of Windows' Notepad. Can you find a tutor
around to help you out with the basic usage of Linux? It's always difficult
to plunge into several different things at the same time, here 'using
linux',
So I started following some tutorials online since I didn't get a response
last time. the tutorial I'm using is:
http://nmr.chem.uu.nl/%7Etsjerk/course/molmod/
I followed that tutorial to the second page and got stuck at the step where
it asks you to input: pdb2gmx -f protein.pdb -o protein.gro -p
It sounds like you dont have the .pdb file in your working directory.
Perhaps you need to learn a bit about unix filesystems
On Sat, Aug 24, 2013 at 6:18 PM, The One And Only chappybo...@gmail.comwrote:
So I started following some tutorials online since I didn't get a response
last time. the
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
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
so how do i solve the protein.pdb issue?
On Sat, Aug 24, 2013 at 6:37 PM, Justin Lemkul jalem...@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
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 chappybo...@gmail.comwrote:
so how do i solve the protein.pdb issue?
On
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