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
cell: +39 3485188790
https://iit.it/people/andrea-spitaleri
ORCID: http://orcid.org/0000-0003-3012-3557
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