Converting between amber md Lennard-Jones parameters and "standard" LJ values
You can find this information elsewhere on the internet, but I find myself searching around each time I encounter this issue. If you dig through the amber force field files, you will find the non-bonded, van der Waals interaction is typically described with the Lennard-Jones potential. They look like this, in a section called MOD4:
ow 1.7683 0.152
These numbers are the LJ parameters for the oxygen in TIP3P water. The spacing may be different, but it will be an atom type and two numbers. These numbers are R_min/2 and ε, in Å and kcal/mol. So, to get the standard σ value, you need to multiply by 2 and divide by 2^(1/6).
So, for the above numbers, you can read off the ε, but conversion of 0.152-that is, 0.152 x 2 x 2^(-1/6)-results in a σ of 3.150752 Å. And, for TIP3P, this value should be 3.1507 Å.