On Mon, Mar 04, 2019, Manyi Yang wrote:
> I am doing the mmpbsa.py to calculate the free energy for
> trajectory. When I constructed the topfile as follow the amber18
> manual and tutorials, and I saw the sentence of "each must have
> the same charges for the same atoms, the same force field must be
> used for all three of the required prmtops, and they must have the
> same PBRadii set " in amber manual for mmpbsa.sy, especially for
> " the same force field must be used for all three of the required
> prmtops". However, I want to combine DNA and small organic molecule
> and construct the corresponding the prmtops. Is it mean that the
> I can not use the leaprc.DNA.bsc1 and leaprc.gaff2 for DNA and
> small organic molecule, respectively? Hence, How can I do for this
> situation?
You are fine....the "same force field" in this instance might be better
written as "the same set of forced fields", or "prepared in the same
manner". Basically, the parameters (including PBRadii) must be
consistent between complex, receptor and ligand prmtop files.
....dac
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Received on Tue Mar 05 2019 - 07:00:02 PST
