Dear AMBER users,
I did a NMR refinment of a drug-DNA complex and acutally the result looks very fine. I used the gaff to simulate the drug and taylored a lot of individual potentials for the drug and incorporated them in the gaff. But for some of them I could not get any reasonable force constants because none of the standard potentials was comparable and I used in these cases arbitrary values of 30 kcal/mol/rad.
Right now I would like to spice the force field up but I don't know whether my approach is reasonable at all. I made sure with a CPMD run at 300 K over for 2 ps, that the drug is in the global minimum and optimized the output B3LYP 6-31+G** with Gaussian03 and calculated frequencies with 6-31+G** .
Actually I don't know exactly how to calculate the force constants but somehow with the Hessian; however, this is another issue. My question is whether my approach does make sense or do I disregard something?
Kind regards
Markus
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Received on Wed Feb 07 2007 - 06:07:13 PST
