On Sat, Oct 22, 2016 at 10:47 PM, Saikat Dutta chowdhury <
pbr322.dutta.gmail.com> wrote:
> Thank you sir for your reply.
>
> But could I use ff14SB in AMBER12 ?
>
You can download AmberTools16. It's free.
http://ambermd.org/AmberTools16-get.html
cheers
Hai
>
> Also is there any problem in using GLYCAM06h with ff99SB-ILDN ?
>
> With regards,
> Saikat
>
>
> On Sun, Oct 23, 2016 at 5:44 AM, David A Case <
> dacase.scarletmail.rutgers.edu> wrote:
>
> > On Sat, Oct 22, 2016, Saikat Dutta chowdhury wrote:
> > >
> > > I have a peptide which contains a HYP (hydroxyproline) residue. I
> wanted
> > to
> > > use ff99SB-ILDN force field and using AMBER12 package. But when I tried
> > to
> > > create the peptide molecule using tleap module I found out that it is
> > > unable to recognize the HYP residue. So I searched for possible answers
> > and
> > > found out that GLYCAM06h has HYP parameters.
> >
> > ff14SB also has HYP parameters (just for HYP and CHYP right now, but you
> > could make an NHYP starting with HYP). Note that the side-chain torsion
> > improvements added in the "ILDN" model are also present in ff14SB (not
> > as identical parameters, but the changes in side chain behavior are very
> > similar.)
> >
> > ....dac
> >
> >
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> >
>
>
>
> --
> Saikat Dutta Chowdhury
> Email: pbr322.dutta.gmail.com
> Mob:
> 8017650842
> 9681144106
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Received on Sat Oct 22 2016 - 22:00:02 PDT
