Thank you David and Pavlína for the information. I got your point. And I
have seen of choosing the force field for protein and DNA is inside the
leaprc.ff14SB.redq file which is reside in the path of $AMBERHOME/dat/leap/cmd
, although its not recommended.
On Tue, Feb 26, 2019 at 8:11 PM Pavlína Pokorná <pokorna.pavlina.ibp.cz>
wrote:
> Hi,
>
> Use both of the force fields You have mentioned, each will describe the
> respective part of Your system. Also read some papers on protein-DNA
> simulations:).
>
> Best,
> Pavlina
>
> On Tue, Feb 26, 2019 at 1:54 PM Sasthi Charan Mandal <
> sasthi.phys.gmail.com>
> wrote:
>
> > Dear sir/madam,
> > I am trying to simulate protein-dna complex. I am preparing the
> > system using ambertools 16. It is saying that for dna the recommended
> force
> > field is bsc1 and for protein ff14SB. So for the protein-dna complex I
> can
> > not find any suitable force field in ambertools tutorial. It would be
> very
> > helpful if someone suggest any force field for the above system.
> >
> > with regards
> > Sasthi
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Received on Tue Feb 26 2019 - 09:30:02 PST
