[gmx-users] re K+ ion

[taveechai taveecharoenkool]

Dear Jochen,
thanks very much for your reply. Anyway, i already did
what you suggest. I can run without the problem. I
want to analyze the system after 1ns or 2ns, when i
use g_saltbr which tell the oppositely two-charged
groups. it doesn't have interaction of K+ and negative
charge. I quite don't understand.. where my K+ charge.


--- Jochen Hub <jhub at gwdg.de> wrote:

> 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
> >forcefield.
> >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
> 
> -- 
> ************************************************
> 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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