[gmx-users] Newbie: How to modify the topology file after adding ions?

[Tsjerk Wassenaar]

Hi Jose,

You're not the first one to follow the tutorial, it does state which
version to use (4.5, see introduction), and it does state how to fix the
topology: editing the file, adding the lines, using the appropriate names.
This tutorial is made to be read and to be thought over.

Of course time flies. The tutorial was written a few years back and ion
naming has changed. You should run genion with -pname Na -nname Cl these
days. And you can use -p, but one of the aims of the tutorial is
familiarizing you with the files, file formats, and components of a
simulation.

The error about the box has nothing to do with the tutorial anymore. You
deviated from a well trodden path, editing the coordinate file, probably
screwing it up...  But please don't blame me for that.

But I take note of the ion issue that hadn't been brought to my attentin
yet. I'll fix it soon.

Best,

Tsjerk

On Dec 7, 2011 8:31 PM, "Jose Borreguero" <borreguero at gmail.com> wrote:

This tutorial doesn't seem to be quite useful, if so many errors pop up.
Maybe it was implemented for Gromacs < 4.5.x but there's no info on the
version it should be used.

However, Lo and behold! I found that you have a nice page with Gromacs
4.5.x tutorials :D  (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html)
I'll give a try with the Lyzosyme one!

- Jose

On Wed, Dec 7, 2011 at 1:29 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote: >
> > > Jose Borreguero ...

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