AMBER Archive (2009)

Subject: Re: [AMBER] How to find a protein's energy

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Sun Sep 06 2009 - 06:49:53 CDT

you need to be more specific about what you want to learn. you can
calculate the energy of a structure, but it has little meaning by
itself since the zero value of energy is arbitrary in molecular
mechanics. what do you want to learn from it?
it's not clear if you know how to use Amber- you don't say. if so, you
can load your prmtop and inpcrd into sander, set imin=1 and nstlim=0.
you will get the energy without minimization. of course you need to
think about what you mean by the "energy": do you want solvation
energy too? and so on.

On Sat, Sep 5, 2009 at 11:48 PM, Ashish Runthala<askamber100_at_gmail.com> wrote:
> I need to find out simply the energy of a protein system.
> How can i know it, before even going for any minimization or dynamics
> studies.
> I need to understand it.
>
> Thanks in advance,
> Ashish
>
> --
> Ashish Runthala,
> Assistant Lecturer,
> Biological Sciences Group,
> Birla Institute of Technology & Science, Pilani,
> INDIA.
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>

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