Thanks for reply.
Bellow is command for generation of restraint file:
makeDIST_RST -upb 7col.dist -pdb gcg_b.amb.pdb -rst RST.dist
So there is requirement of pdb & 7col.dist (file look like:- 1 GUA H1' 1
GUA H3' 4.6), here 4.6 is upper bond so from where this upper bond value
comes, similarly in torsion angle restraint:- lower_bond and upper_bond.
With regards
sangita
On 2013-08-21 17:33, Jason Swails wrote:
> 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 hig h 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
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Received on Thu Aug 22 2013 - 05:00:02 PDT
