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

[Jernej Zidar]

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.

  Any recommendations or experiences?

Thanks in advance!

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

[Paulo Netz]

Hi Jernej

I'll choose AMBER or CHARMM, because these two forcefields
have a more reliable description of nucleic acids. In my experience,
OPLS-aa and GROMOS do not seem to be able to produce stable
simulations in the large time scale for nucleic acids systems.

Best regards

Paulo Netz


2015-02-02 2:53 GMT+01:00 Jernej Zidar :

> 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.
>
>   Any recommendations or experiences?
>
> Thanks in advance!
>
> Jernej
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> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] DNA-protein complex - which force field to use?

[Erik Marklund]

On 2 Feb 2015, at 01:53, Jernej Zidar 
mailto:jernej.zi...@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

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

[Felipe Merino]

Hi,

On 02/02/15 10:18, Erik Marklund wrote:


On 2 Feb 2015, at 01:53, Jernej Zidar 
mailto:jernej.zi...@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.


Best

Felipe

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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