Hi all,
This might be something of a long shot since I'm digging deep into history here, but does anyone know how ff86 handles nucleosides? I'm doing an exercise to see how close I can feasibly get to the nucleoside charges in ff94 by Cieplak et al's paper, and had a quick question on how the minimization was done on the nucleosides- specifically, it says
The nucleosides were optimized using the molecular mechanical AMBER program and its force field
Referring to Weiner et al forcefields. I'm assuming at the time, ff86 was used to describe the nucleosides, but I can't figure out how to actually make a nucleoside in ff86, ie in the modern forcefields, I'd just call on DXN for the appropriate one. But when I feed in a structure of adenosine for example, as
ATOM 1 H HB 1 0.226 1.803 -1.743 1.00 0.00 H
ATOM 2 O5'DADE 2 0.998 1.358 -1.387 1.00 0.00 O
...
ATOM 30 O3'DADE 2 3.252 -1.926 0.351 1.00 0.00 O
ATOM 31 H HE 3 3.096 -2.283 1.228 1.00 0.00 H
I noticed the net charge is nonzero- as per Figure 2 of the Weiner paper, it shows the O5' and O3' for terminating ends should be -0.404 and -0.506, which doesn't seem to match the O5'/O3' charges in ff86 (-0.509) for internal bases. The part I'm puzzled on is I can't find an actual entry for terminal O5/O3' charges in the forcefield, so is it just a case where I should 'swap' them for the terminal end charges to make the nucleoside?
Best,
Kenneth
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Received on Wed Dec 02 2020 - 14:30:02 PST
