[gmx-users] K ion

Jochen Hub jhub at gwdg.de
Wed Jan 18 17:02:31 CET 2006

taveechai taveecharoenkool wrote:

>Dear all,
> I want to study the effect of K ion on a protein. I
>add this line in ions.itp 
> [ moleculetype ]
>; molname	nrexcl
>K+		1
>[ atoms ]
>; id	at type res nr	residu name	at name  cg nr  charge
>  mass
>1	K+	1	K+		K	1	1	 39.0983  
>it seems ok, i can run (mdrun) without error. The
>thing in my mind is that is it enough (to edit only
>one file) cos it seems like K+ doesn't contain
>positive charge when i used g_saltbr? i use Gromos96
>Thanks in advance

You should add a
K+      1

into the [ molecules ] section of your topol.top.

And , of course, you need to place it into your starting structure (pdb 
or gro).


Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de

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