On 21/08/2012 2:30 PM, Yun Shi wrote:
Hello all,
I am simulating protein-ligand complex with amber99sb force field in
TIP3P water. What would be a reasonable value rvdw? I saw someone
uses 1.0, and I did not find any abnormality when using 1.4 nm for
rvdw, but where can I find the right
In the original paper [Comparison of multiple Amber force fields and
development of improved protein backbone parameters], 0.8 nm was used;
but I did find recent papers using 1.0 nm for rvdw. And I myself used
1.4 nm, all without obvious abnormality.
On Mon, Aug 20, 2012 at 10:13 PM, Mark Abraham
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