Hi Carlos,
No I don't use the existing force fields with EP. I just add EP based on GAFF parameters to examine the halogen bond effect in hydration free energy calculation. In this way, how can I prepare the input files correctly?
Thanks in advance!
Mingjun
> -----原始邮件-----
> 发件人: "Carlos Simmerling" <carlos.simmerling.gmail.com>
> 发送时间: 2020-03-14 23:18:40 (星期六)
> 收件人: "AMBER Mailing List" <amber.ambermd.org>
> 抄送:
> 主题: Re: [AMBER] Lone Pairs in AMBER FF
>
> Lone pairs are only modeled in a few force fields. Are you using one that
> includes them?
>
> On Sat, Mar 14, 2020, 10:35 AM 杨明俊 <mjyang.dicp.ac.cn> wrote:
>
> > Hi All,
> >
> >
> > I am trying to use AMBER18 to compute the hydration free energy of
> > halogen substituted benzene with lone pairs. However, I can only get some
> > information in section 17.7.4 of amber manual. In the manual, it says that
> > the bonded terms are not computed with "frameon = 1" and only nonbonded
> > (ele) terms will be computed.I have two questions to confirm in order to
> > know how to prepare the input files (mol2 and frcmod) correctly:
> > 1. how the position of the lone pair is determined from the input mol2 and
> > frcmod files?
> > 2. how does the lone pair evolve during MD simulations? Although in the
> > manual it says "The lone pairs are kept in ideal geometry relative to local
> > atoms, and resulting torques are transferred to these atoms", I still don't
> > understand how it does in the code.
> >
> >
> > Any of your information about getting better understanding of this
> > question is appreciated!
> > Thanks in advance!
> >
> >
> > Mingjun
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> >
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Received on Sat Mar 14 2020 - 20:30:02 PDT
