AMBER Archive (2005)

Subject: Re: AMBER: fail of minimization in sander

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Thu Jun 16 2005 - 06:06:42 CDT

10-12 refers to the form of the potential energy function. you might
want to do some background
reading on this, since modifying parameters really requires some knowledge
of how the energy function works. I suggest "Molecular Modelling" by Andrew
Leach. Explaining the energy functions is beyond the scope of getting help
by email, and since those descriptions already exist there is no reason
to duplicate them here.
good luck!

wendy wrote:

> In fact I have no idea what is the meaning of " non-zero 10-12
> coefficient". There are a lots of parameters in my modified set. Even
> the parameters I modifed are more than 10-12.
>
> I modify the parameters with Xleap in the way Amber Tutorial 4 does.
> Can you give me more suggestions?
>
> Thank you very much!!
>
>
>
> Wendy

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