Andrew,
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.
Cheers,
Josh
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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