If I source leaprc.ff12SB,ions08.lib and solvents.lib will be loaded. Whether it's okay to apply them to my ligands(Na+,Cl-,H2O) when I want to calculate PMF.
------------------ Original ------------------
From: "carlos.simmerling";<carlos.simmerling.gmail.com>;
Date: Mon, Apr 11, 2016 09:50 PM
To: "AMBER Mailing List"<amber.ambermd.org>;
Subject: Re: [AMBER] ff12SB force field
I don't really understand your question. ff12SB is for proteins, and is not
related to the "(Cl- or Na+ or H2O)" that you mention. If you are
simulating proteins, we suggest the newer ff14SB. If you have a question
about the force field, can you try to be more specific about your concern?
On Mon, Apr 11, 2016 at 9:47 AM, wjli <wenjuanli93.gmail.com> wrote:
> Dear Amber members,
>
> I want to calculate PMF profiles for ligands(Cl- or Na+ or H2O) via tunnel
> . I hesitate about the property of using ff12SB force field,just like
> applying water box's force field(TIP3PBOX) to ligand water.
>
> I will very appreciate if anyone can offer some suggestions.
>
> Look forward to your reply!
> Best wishes.
> wjli
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>
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Received on Mon Apr 11 2016 - 07:30:04 PDT
