[gmx-users] Help with simulation

David van der Spoel spoel at xray.bmc.uu.se
Fri Nov 14 16:16:01 CET 2003

On Fri, 2003-11-14 at 16:00, Jodi Fangman wrote:
> Hello,
> I am a relatively new gromacs user and have run into a problem. I am trying to 
> simulate a small protein in solution to examine side-chain rotomer 
> distributions. I have been able to run the simulation in water but would like 
> to run it with ions as well. I was able to add the number of ions I wanted 
> using genion without any problems. I then changed my *.top file to the new 
> number of waters and added the ions. I also added the ions.itp reference in 
> this file. When I try to run the simulation with the ions included I receive an 
> error message. The error message says: FATAL ERROR no such atomtype 'K'. This 
> is the error I receive whether I am using potassium or sodium as my positive 
> ion. I can not figure out what is going wrong. Have I miss entered/referenced 
> something? Will my forcefield not recognize ions? (I am using the GROMACS 
> forcefield with all hydrogens) Or is there a different problem that I am not 
> aware of? Thank you for any help you can provide.
you're probably better off with either the GROMOS43a1 force field or the
OPLS force field. Both have support for Potassium IIRC, but it may be
named K+

> Sincerely 
> Jodi Fangman
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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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