On Sat, Jan 18, 2020, Karolina Mitusińska (Markowska) wrote:
>
>I've played with the POL3 water model and discovered something odd.
>I'm using a system with additional crystallographic water molecules. And no
>matter what they are called in the pdb file, they are treated different
>than the water molecules from the POL3BOX.
How do you know that there is more than a cosmetic difference? Have you
used parmed to print the bonds and angles for the two waters? Are there
hydrogens on the waters in the protein_with_wat.pdb?
My guess is that *very* few people have used ipol=1 in Amber recently,
and the ones that have done this probably are not following this list.
So you may expect to have to do a lot of sleuthing around to get a
non-polarizable protein + polarizable water system to work.
Have you looked at the test cases for ipol=1? Can you run those
successfully, and maybe extend or modify them? That would give you
something to compare with what you are doing.
....dac
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Received on Sun Jan 19 2020 - 18:00:02 PST
