[gmx-users] Protein-DNA_ligand simulation.

[Andrea Spitaleri]

You can think to use AMBER14SB too which contains the stable bsc0 
parameters:

"Uses frcmod.ff14SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA"

or as Justin suggested the new bsc1 from Orozco

http://www.nature.com/nmeth/journal/v13/n1/full/nmeth.3658.html

http://mmb.irbbarcelona.org/BigNASim/help.php?id=download

HTH

and


On 22/11/2016 21:24, Justin Lemkul wrote:
>
>
> On 11/22/16 2:06 PM, maria khan wrote:
>> Dear Gromacs users.
>> Can gromacs is used in Protein -DNA-ligand simulation??f it is used, 
>> which
>> forcefield will be used.??
>
> Just about any will work, but CHARMM and AMBER are most commonly used 
> for systems like these.  You should investigate (in the literature) 
> the suitability of current parameter sets in light of how they might 
> affect properties of interest (e.g. AMBER99 is a bad choice for DNA 
> because it distorts over time, but more recent parmbsc1 is good, 
> similarly CHARMM36 is vastly better than CHARMM27 for nucleic acids).
>
>> what will be the method for that type of simulation.kindly answer me in
>> detail.
>
> Simulating a protein-DNA complex is no different from a protein in 
> water. You've got a biomolecule in aqueous solvent.  The protocol is 
> generally the same.
>
> -Justin
>

-- 
Andrea Spitaleri PhD
Computational mOdelling of NanosCalE and bioPhysical sysTems - CONCEPT Lab
ISTITUTO ITALIANO DI TECNOLOGIA
Via Morego 30, 16163 - Genova, Italy
https://iit.it/research/lines/computational-modelling-of-nanoscale-and-biophysical-systems
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https://iit.it/people/andrea-spitaleri
ORCID: http://orcid.org/0000-0003-3012-3557