VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Mon Apr 24 2006 - 02:15:31 CDT

Hi Jean,

As far as I know, you can build a double helix DNA using the program
Insight II (it contains a module called "biopolymer"). The problem is
that this software is not free. The other program you may use is
called "Hyperchem". You also have to pay for this software, but the
main difference is that you can download a trial version and
(hopefully) you'll have enough time to build your structure.

Regarding energy minimization, you can use NAMD + CHARMM 27 topology
and parameters.

Hope it helps,

Cheers,

Michel

2006/4/24, Jean Richelle <jean.richelle_at_ulb.ac.be>:
> Hi,
>
> Does anyone knows about a free software to build (automatically) a
> DNA double helix fragment having the standard B-DNA conformation ?
>
> And I have a second question. Does anyone knows about a software
> that do energy minimization on DNA double helix ? (I mean that it
> must already hav all the parameters fixed for DNA) I have a 29 bp
> long helix, but I have the impression that it could be more straight,
> and I wonder if I could achieve that by energy minimization.
>
> Regards,
>
> Jean
>