Thank you very much!
Lei
> 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.rosswalker.co.uk
> <mailto:ross.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.rosswalker.co.uk
> <mailto:ross.rosswalker.co.uk> |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery,
> may not
> be read every day, and should not be used for urgent or sensitive
> issues.
>
>
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Received on Wed Jun 06 2007 - 06:07:22 PDT
