Re: [AMBER] ff99SB with nmr and ildn corrections

From: case <>
Date: Wed, 27 Nov 2013 21:31:07 -0500

On Wed, Nov 27, 2013, Norah Schlacter wrote:
> What is the consensus about the order of loading the parameters files to
> obtain ildn and nmr corrections on the ff99SB force field? I know things
> overwrite according to the order they are loaded so I am a little
> confused about loading/sourcing which files to load in which order.

Parameters in files loaded earlier will be overwritten by parameters in files
loaded later.

> Should we still load ions08.lib separately?

This is done already in many of the leaprc files; if not, you may need to do
it yourself.

> Are those corrections compatible with frcmod.ionsjc_tip3p

yes...of course you have to be using tip3p water (d'oh). I'd recommend
looking inside the ions08.lib file, so you will understand what it contains
(if you've not already done that).

> and GB7+PBradii bondi?

GB was originally developed with the idea that ions as well as water molecules
would be part of the implicit solvent. Lots of people seem to want to run
GB with explicit ions, but I don't know of any careful evaluation of the
parameters that would be needed to make this work well. Since this is not a
"standard" Amber option, it's up to you to make sure that you have the desired
parameters (maybe taking them from some publication you like; or testing
various options yourself.)


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Received on Wed Nov 27 2013 - 19:00:02 PST
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