Dear David and Francois,
Thank you so much for your response.
Yes David, I have in fact looked into the contributed parameter
database where they have defined a new Atom Type for "O3" for the
terminal phosphate oxygens. But as I was looking at using GAFF force
field for generating the forcefield parameters via antechamber, I was
contemplating if there is a current atom type for phosphate specific
bound oxygen just in case I have missed something.
And as Francois mentions, I also think it is a matter of computing a
new tom type. I believe it will be reasonably accurate for my
calculation with the current atom type definition. In the F-90
project, i see that "OS" and "O2" atom type are used from the
AMBER99SB force field for the phosphate bound oxygens which is similar
to using "os" and "o" in the GAFF fore field.
Regards,
Dilraj.
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Received on Tue Jun 19 2012 - 06:30:03 PDT
