[gmx-users] Protein-DNA_ligand simulation.
andrea.spitaleri at iit.it
Tue Nov 22 21:43:36 CET 2016
You can think to use AMBER14SB too which contains the stable bsc0
"Uses frcmod.ff14SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA"
or as Justin suggested the new bsc1 from Orozco
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,
>> 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
> 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.
Andrea Spitaleri PhD
Computational mOdelling of NanosCalE and bioPhysical sysTems - CONCEPT Lab
ISTITUTO ITALIANO DI TECNOLOGIA
Via Morego 30, 16163 - Genova, Italy
cell: +39 3485188790
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