[gmx-users] genion command with PDB files for amber03 force field

Joshua Ballanco jballanc at gmail.com
Sun Mar 8 22:34:56 CET 2009


Just ran into this myself. If you read the notes on http://chemistry.csulb.edu/ffamber/#usage 
  closely, you'll find this little tid-bit:

> "If you are using ion-related GROMACS tools, such as genion, you  
> will need to enter the AMBER ion definition to the ions.itp file in  
> the "top" directory of the GROMACS distribution."

This isn't too tough, as all the parameters for the ions are included  
with the Amber ports, but genion needs them to be in the ions.itp (or  
other suitable) file.



On Mar 5, 2009, at 9:44 AM, drugdesign wrote:

> Dear gromacs users,
> I am using genion command to add ions to .tpr file which
> was made for protein by use of amber03 force field.
> In intial pdb file N-terminal amino acid is NHIE, but genion changes  
> it to NHI, which isnot recognized by next pdb2gmx.
> This is not a big problem , but it looks is a little bit like a bug.
> Best regards,
> Andrew
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