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

From: Liang, Lei <>
Date: Mon, 04 Jun 2007 16:02:04 -0500

Thank you very much for the reply and advices!

> 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:- |
> | | 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.
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to
> To unsubscribe, send "unsubscribe amber" to

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Jun 06 2007 - 06:07:22 PDT
Custom Search