[gmx-users] K+ ion adding problem

[Venky Krishna]

Thanks Brian

~Venky

Venkatramanan Krishnamani
Dr.Janos K. Lanyi Lab,
D320, Medical Sciences D
University of California, Irvine

On Jul 11, 2005, at 3:46 PM, Brian Stephenson wrote:

> Venky,
>
> 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 error.
>
> -Brian
>
>
>
> 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.
>>
>> Thanks
>>
>> Venky
>>
>> --
>> Venkatramanan Krishnamani
>> Graduate Student,
>> Dr. Janos K. Lanyi Lab
>> Univerisity of California, Irvine
>> Irvine, CA
>> (949) 232-3021
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>
>