Dear Hai,
so it is enough for simulating RNA and protein together or is better to use
the ff99SB?
Thanks and regards,
Mahad
2015-08-05 14:48 GMT+02:00 Hai Nguyen <nhai.qn.gmail.com>:
> 'source leaprc.ff14SB' will load protein 14SB ff + DNA bsc0 + RNA chiOL3.
> You can try can look at the log file from tleap.
>
> But I admit that using `ff14SB` name is a bit confusing.
>
> Hai
>
> On Wed, Aug 5, 2015 at 3:35 AM, Pragya Priyadarshini <pragya.imtech.res.in
> >
> wrote:
>
> >
> >
> > Dear Amber users,
> >
> > I have to do MD simulation of protein-DNA complex, earlier I have used
> > ff99SB + bsc0 force field of AMBER11, now I have to use AMBER 14 for my
> > study. For protein, it is mentioned in AMBER14 manual, to use ff14SB but
> > I am not getting about DNA. Is ff14SB, sufficient for DNA of protein-DNA
> > complex or I have to other force field.
> >
> > Please suggest me.
> >
> > Regards
> >
> > --
> > Pragya Priyadarshini
> >
> > C/o Dr. Balvinder Singh
> > Bioinformatics Center (G N R P C)
> > Institute of Microbial Technology-CSIR
> > Sector 39A, Chandigarh-160036, INDIA
> >
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> >
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Received on Wed Aug 05 2015 - 06:30:02 PDT
