[gmx-users] Help with simulation

[David van der Spoel]

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.
________________________________________________________________________
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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