AMBER Archive (2007)

Subject: Re: AMBER: Problem about prepare the model when running antechamber

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Jun 04 2007 - 15:52:23 CDT

you might especially want to look at this article:

S. Park, R. Radmer, T. Klein, V. S. Pande. New parameters for collagen
simulation. *Journal of Computational Chemistry, **26 *1612-6 (2005)

On 6/4/07, Ross Walker <ross_at_rosswalker.co.uk> wrote:
>
> Hi
>
> > I ran antechamber to parameterize my molecule consists of 1125 atoms.
>
> This is way beyond the capabilities of antechamber and even if you could
> modify it to work your chances of obtaining a decent set of charges and
> parameters is close to nil. You should read up on the RESP method for
> calculating charges so that you are familiar with it and more importantly
> with it's limitations. Such grid based methods never do well with buried
> atoms and in your case with 1125 atoms I suspect a large number of them
> are
> buried and so will likely be assigned non-realistic charges. Add to this
> the
> fact that you need to run QM calculations on this entire system and you
> should start to see the problem.
>
> I strongly urge you to search the literature for previous work on collagen
> models, then look at carefully parameterizing this system, including
> breaking it down into manageable (and meaningful) chunks and then manually
> assigning atom types and developing suitable parameters yourself.
>
> This will require a considerable amount of effort but unfortunately there
> is
> no magic bullet in this field.
>
> Good luck.
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
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>
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