[gmx-users] Newbie question
tsjerkw at gmail.com
Mon Jun 23 22:01:04 CEST 2008
Of course I can't add anything to the comments regarding the solvent and ions ;)
The #include "ions.itp" is commonly added through pdb2gmx in the >3.1
versions, so it shouldn't be necessary to add that (and it isn't for
the tutorial (v3.3.3). Anyway, it's good to keep in mind though that
the ions have to be defined. I'm taking note of these issues to
improve the tutorial (still being a work in progress; any comments
That there are two solvent entries under [ system ] is due to the
keeping of water from the crystal structure. This poses a problem for
the -p option of genion, which should be able to edit the topology,
but it will add the ions for each solvent entry... (this could be
considered a bug...). But next to being safe, it's also good to get a
bit of the feel of the inside of the topology file :)
On Mon, Jun 23, 2008 at 3:48 PM, Marcus Kubitzki <mkubitz at gwdg.de> wrote:
> Hi Andres,
> in total you have 10475 (198+10277) SOL molecules, so you can condense
> the two SOL lines into one. Suppose you add 20 NA+ and 20 CL-, you
> subtract 40 SOL molecules from the system and add 40 ions in total. So
> you write:
> [ molecules ]
> ; Compound #mols
> Protein_A 1
> SOL 10435
> NA+ 20
> CL- 20
> There are now 40 SOL molecules less (10475-30=10435) and the ions are
> added. Don't forget to add an #include "ions.itp" under
> "Include generic topology for ions"
> Andres Rojas Guerrero wrote:
>> Hi, I'm newbie in Gromacs and MD, I'm reading the Tsjerk excellent
>> tutorial. In the part of Addition of Ions, Tsjerk said that we need to
>> edit the topology file and the decrease the number of solvent molecules,
>> and add a line specifying the number Na+ and Cl-. How can I do this?
>> Let me explain, in the topology file I have:
>> [ molecules ]
>> 10565 ; Compound #mols
>> 10566 Protein_A 1
>> 10567 SOL 198
>> 10568 SOL 10277
>> What number I need to change? and what it's the fomat to add the ions
>> Na+ and Cl- to topology file?
>> Thank you very much.
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> Dr. Marcus Kubitzki
> Max Planck Institute for Biophysical Chemistry
> Computational Biomolecular Dynamics Group
> Am Fassberg 11
> D-37077 Göttingen
> phone: ++49-551-2012312
> fax: ++49-551-2012302
> Email: mkubitz[at]gwdg.de
> www: http://www.mpibpc.mpg.de/groups/de_groot/
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
3584 CH Utrecht
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