[gmx-users] DNA-protein complex - which force field to use?

Felipe Merino felipe.merino at mpi-dortmund.mpg.de
Mon Feb 2 10:57:00 CET 2015


On 02/02/15 10:18, Erik Marklund wrote:
> On 2 Feb 2015, at 01:53, Jernej Zidar <jernej.zidar at gmail.com<mailto:jernej.zidar at gmail.com>> wrote:
> Hi everyone!
>   I would like to study a DNA-protein complex. The protein part is
> composed of aminoacids covalently attached to the DNA bases. Which
> force field would you recommend? Based on recent experience I was
> thinking of using either OPLS-aa or CHARMM. OPLS-aa would be the
> prefered choice because it performs way better than CHARMM.
> At least for proteins that seems incorrect
> http://pubs.acs.org/doi/full/10.1021/ct2007814
The comparison here is with an old version of CHARMM. CHARMM36 is 
supposed to be way better now. In any case, If you are working with DNA 
the best choice seems to still be Amber-ff99sb with the bsc0 correction. 
I would actually use something like Amber-ff99sb*-ildn-bsc0. All those 
modifications are already available to be read in gromacs around.


> Kind regards,
> Erik
> Erik Marklund, PhD
> Postdoctoral Research Fellow, Fulford JRF
> Department of Chemistry
> Physical & Theoretical Chemistry Laboratory
> University of Oxford
> South Parks Road
> Oxford
> OX1 3QZ
>   Any recommendations or experiences?
> Thanks in advance!
> Jernej
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