Dear Amber Users,
Please excuse me if this has been discussed before
in the mailing list. I could not come across a very satisfactory
conclusion and hence am posting this in the list to get your feedback.
I am currently setting up a system for simulation which a ligand
molecule consisting of a tri-phosphate group similar to ATP and GTP. I
used the antechamber from Amber11 and looked into the atom type
definition for the ligand atoms. For the atoms bound to the phosphate,
they are defined as either "o" or "os".
If I look at the gaff atom force field definition,
o-sp2 oxygen in C=O, COO-
os-sp3 oxygen in ethers and esters
Now I am fine with the hybridisation state definition of the atoms and
hence the corresponding atom type definition in my ligand.
However, I was wandering if this is the current state of atom-type
definition for the phosphate bound atoms in the GAFF parameters? And
if this is a reasonable definition for our calculations.
Will be glad to hear from you all.
Thank you,
Dilraj.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 18 2012 - 04:30:02 PDT
