[gmx-users] N/A

[Mark Abraham]

Florian Haberl wrote:
> hi,
> 
> On Friday 19 January 2007 15:25, sangeeta wrote:
>> Dear Sir,
>>
>>      I have three questions,
>>
>>      My protein has +2 charge, so I added two Cl atoms through the program
>> genion and subsequently edited the  topol.top file, in spite of that while
>> running mdrun it gave an error that  "FATAL error, CL atom type can not be
>> found",I can not understand the problem.
> 
> You have to add it to your .mdp file, too.

I think not. The problem here is that your forcefield doesn't have a CL 
atom type defined. You will need to #include "ions.itp" in your .top 
file, and that will need to have a correct definition for Cl- for your 
force field and match the atom name in your .top file.

Mark