On Thu, Aug 22, 2013, 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 don't think anyone on the list is likely to be of much help. I'm not sure
what you mean by an unusal non-covalent bond, nor do I need to know. If you
wish to make up an artificial constraint to try to prevent this, you will
have to decide how to do that on your own, as far as I can see. It does not
sound like any kind of standard calculation.
> I am not getting how
> >> to define upper_bond in "Distance restraint"
This is hard to follow: the upper bound is a floating point number that
represents an upper bound on the corresponding distance. When you say that
you do not know how to define it, it's hard to understand exactly what you
mean: is it that you don't know what value to type in? If so, see above.
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 22 2013 - 19:30:03 PDT
