On Mon, Apr 30, 2018, Khabiri, Morteza wrote:
>
> Is it still possible to do thermodynamic integration in Amber using
> no-softcore potential by sander?
Sure. If you don't set ifsc, you won't get softcore potentials. Note:
there is no reason to use softcore unless you have atoms that appear or
disappear between the two end states.
>
> As I have seen some tleap options like pertName are no longer exist in amber.
I'm not sure where you are getting this: sander has always used two
separate prmtop files, one for state 0 and one for state 1. Neither
would use pertxxxx -type parameters. [The idea of using "pert"
variables to define two states in a single prmtop file was abandoned
15-20 years ago.]
>
> Is there any tutorial for TI calculations with no-softcore?
Yes: http://ambermd.org/tutorials/shirts/index.html
Please read the introduction carefully: this is an old tutorial, made
before softcore potentials were implemented. But it should still work.
(You don't say *why* you want to avoid softcores....)
....dac
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Received on Mon Apr 30 2018 - 17:30:04 PDT
