On Fri, Jul 03, 2020, Loki wrote:
>
>
>>> # to use ions for TIP5P, you will need to use a different frcmod below
>>> # If desired, see the AMBER manual for additional ion force field
>options.
>>> ionsff = loadamberparams frcmod.ionsjc_tip3p # set ion params for TIP3P
>Loading parameters: /s/amber/amber18/CentOS7/amber18/dat/leap/parm/frcmod.
>ionsjc_tip3p
This comes from the GLYCAM_06j-1 leaprc file. It's a hold-over from earlier
days when water/ion models were loaded along with macromolecule force fields
in the same leaprc file. If you don't trust your ability to use parmed
to find out what parameters are actually getting loaded, just comment out the
water and ions lines in leaprc.GLYCAM_06-j, and load water models yourself.
(I'm not sure that much or any testing has ever been done on the combination
of GLYCAM with OPC water, but it's probably no big disaster.)
>
>Why are those read?
Not sure the "those" refers to in this context.
>
>Lastly, is the 12-6 LJ potential used for the OPC water model (and any 3
>point charge rigid model)?
The LJ potential is used for all water models in Amber (other than amoeba).
....dac
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Received on Wed Jul 08 2020 - 10:00:04 PDT
