On Wed, Feb 20, 2019, Sunita Patel wrote:
>
>I have to run my simulations in amber12 using amber ff99SB force field for
>comparison purpose. I tried using source leaprc.tip3p."
>but it didn't recognize the Ca2+ ions.
>I need your guidance please to add Ca2+.
Upgrade to AmberTools18. We didn't offer "standard" force fields for
multivalent ions seven years ago. Plus, it's really hard to recommend
that you use ff99SB (created 13 years ago) for the protein. Upgrading
that is needed as well. (I guess if it is "for comparison", you might
have a justification for using ff99SB; but be sure you are going to
learn something. Note that, for a given prmtop file, MD results from
amber12 and from current Amber versions give equivalent results. Also,
you can prepare the prmtop file using AmberTools18, then run the
simualtion with pmemd from amber12 if you feel you need to.)
....dac
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Received on Wed Feb 20 2019 - 08:00:02 PST
