On Wed, Aug 21, 2013 at 1:27 AM, <sangita.imtech.res.in> wrote:
>
>
> Hello All
>
> I am doing MD simulation of protein-DNA complex but at the beginning of
> production run there is high fluctuation of terminal end residue as a
> result it is making unusual non covalent bond with another residue (not
> observed in crystal structure) also affecting other non covalent bonds.
> To resolve it I want to use NMR restraint so that it will show little
> fluctuation.
>
> I amber tutorial there is a tutorial for NMR restraint, generation of
> distance & torsion angle restraint is already defined here.
>
> Distance_restraint:-
>
> 1
>
> st
>
> _res# 1
>
> st
>
> _res_name 1
>
> st
>
> _atom_name 2
>
> nd
>
> _res# 2
>
> nd
>
> _res_name 2
>
> nd
>
> _atom_name upper_bound
>
> Torsion angle restraint:-
>
> res# res_name torsion_name lower_bound upper_bound
>
> But here I am not getting how to define upper_bond in "Distance
> restraint" and lower_bond and upper_bond in "Torsion angle restraint"
The above does not look familiar to me (but perhaps something happened to
the formatting of the email?). In any case, you can apply distance, angle,
or torsion restraints using the NMR restraints built into Amber. See the
section about them in the Amber manual (Chapter 6, section 1, page 200 of
the Amber12 manual) for more instruction.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Aug 21 2013 - 05:30:02 PDT
