[gmx-users] K+ ion adding problem

Brian Stephenson bcstephe at MIT.EDU
Tue Jul 12 00:46:37 CEST 2005


You must refer to the K ion using exactly the same name that it is referred 
to in the ions.itp file.  This varies depending on the
FF you are using.  If you look in the ions.itp file in gromacs/share/top/ 
it is K for _FF_GROMACS, K+ in _FF_OPLS, etc.  I
don't think you need to include a define = D_FF_OPLS at the top of your 
.mdp file for the program to know which forcefield to
access . . . including the .itp file associated with the forcefield you're 
using in your .top file should be sufficient.  However, you
could try that if it still gives you problems.

Also there is a -pname option (for cations) and -nname (for anions) with 
genion.  I believe if you don't insert the ions with the
same name that you call them with later you get a warning, but not a fatal 


At 02:45 PM 7/11/2005 -0700, you wrote:
>Hi all,
>My system consists of one Protein molecule and 13619 solvent molecules. I 
>tried adding 100mM KCl to the system which worked out to be 24 atoms...the 
>genion command executed perfectly. but I am not further able to generate a 
>topology for this ion added pdb file. I modified the top files lines to
>[ molecules ]
>; Compound        #mols
>Protein_A            1
>SOL             13595
>K                      24
>and also included "ions.itp" file in the topology file.
>but when i execute the grompp command I get a error message
>"Fatal error: No such moleculetype K"
>Please advice me to troubleshoot this problem.
>Venkatramanan Krishnamani
>Graduate Student,
>Dr. Janos K. Lanyi Lab
>Univerisity of California, Irvine
>Irvine, CA
>(949) 232-3021
>gmx-users mailing list
>gmx-users at gromacs.org
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