[gmx-users] K+ gain

David spoel at xray.bmc.uu.se
Tue Jul 8 09:16:02 CEST 2003

On Tue, 2003-07-08 at 09:07, Semen Esilevsky wrote:
> Hi all,
> I'm just started using GROMACS and thus have a lot of
> questions. The current one is the following:
> I've tried to simulate the much abused KcsA potassium
> channel containing 3 K+ ions in the structure. I've
> got the message "unknown residue type: K" when runing
> pdb2gmx. But there IS K+ in the force-field files! 
> I've found several postings reporting this problem and
> even ions.itp file correcting it. The problem is that
> I can't understand where to place it.
> The only way I've found is to assign all K+ parameters
> to Rb+ and manually change K+ to Rb+ in .pdb (stupid,
> but working)
> Could someone explain in details how to deal with this
> problem?
No, but it could be as simple as renaming K to K+ in your pdb file.
Otherwise your solution is fine too, as long as you check and double
check that you're using the right force field parameters...
(that is, use gmxdump to check the Lennard Jones parameters for your K+)

Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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