Date: Wed Nov 26 2003 - 00:14:37 CST
I want to do MD calculation with NAMD program and CHARMM force field. There is a
novel molecule"phosphonate" in my system. I need generate its force field
parameter. In CHARMM force field, there are many parameters for nucleic acid. So I
can copy many parameters from nucleic acid. However my phosphonate includes bond
P-C which nucleic acid have not( it only have bond P-O). Therefore I have to
generate the parameters for those including bond P-C such as Kb and b0 in V(bond)
= Kb(b - b0)**2, Ktheta and Theta0 in V(angle) = Ktheta(Theta - Theta0)**2 etc.
Would you like to give me some advice on these parameter? How should I get these
parameters? Or Where can I find these parameter?
Thank you very much!
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