AMBER Archive (2006)

Subject: Re: AMBER: EEL and 1-4 EEL; VDWAALS and 1-4 VDWAALS

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Thu Jan 12 2006 - 16:00:24 CST

Dear Carlos,

Thanks for your response. The reason why I asked the question is to see
where and how the e&s interaction is used. I thought that the e&s energy
included all the e&s interactions; 1-2, 1-3, 1-4, etc... But I think that
this is not the case in AMBER force field. The 1-2, 1-3 e&s interactions
are incorporated in the bond and angle terms.

So, in reality, the meaning of e&s interaction in AMBER force field is
including the 1-4, 1-5, 1-6, etc. interactions and the e&s intermolecular
interactions, is that right?

Best,

On Thu, 12 Jan 2006, Carlos Simmerling wrote:

>
> >After minimization, the .out file has the decomposed energies for each
> >step, such as BOND, ANGLE, DIHED, VDWAALS, EEL, HBOND, 1-4 VDW, 1-4 EEL,
> >RESTRAINT, etc. As far as I understood, EEL is the electrostatic energy,
> >which excludes the electrostatic energies of the 1-4 interactions, am I
> >right?
> >
> yes
>
> >If yes, what is the importance of 1-4 EEL?
> >
> what do you mean by "importance"? they are interactions between
> atoms separated by 3 bonds (1-4 pairs).
>
> >And the same goes for
> >VDWALLS energy; what would be the importance of the 1-4 VDW?
> >
> >
> >
> same as 1-4 EEL but for vdw.
> if these don't answer the questions then let us know more specifically
> what you mean.
>
> >Best,
> >
> >
> >
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-- 
  Ilyas Yildirim
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