AMBER Archive (2005)

Subject: Re: AMBER: infinite DNA

From: David A. Case (case_at_scripps.edu)
Date: Fri Jul 08 2005 - 19:26:04 CDT

On Fri, Jul 08, 2005, Carlos Simmerling wrote:

> Stern, Julie wrote:

> > I'm trying to make some infinite DNA. Has anyone
> >done this and can make suggestions for approaches and
> >pitfalls to watch out for? Or, even if you haven't done
> >it, can anyone suggest what to look for or pointers to
> >useful info?

> search the archives, this has been discussed before... I don't
> recall the details though. sometime in the past year. there was
> discussion about how to add the bonds to the images.

Well, you could find this message:

    http://amber.ch.ic.ac.uk/archive/200311/0037.html

which basically tells you (correctly) that this cannot be done without code
modifications. Amber doesn't allow bonds to cross between unit cells.
The "fix" is not all that complicated, but definitely would require a fair
amount of work from someone who understood with sander or pmemd.

(Note: Tom Bishop reports getting this to work in NAMD, using amber prmtop
files, and hence [I assume] the Amber force field:

     http://amber.ch.ic.ac.uk/archive/200310/0090.html )

....dac

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