Thanks Charles. Charles and group: it became a problem in practice
for me because I was using the NOE potential for negative PRE
restraints on extended chains longer than 99 angstroms. A spin label on
one end of the chain will often not enhance the relaxation of many protons at
the other end of the chain and this lack of enhancement should be, or has
been, used as negative restraints between chain ends. Another
nice thing I stumbled upon when using the NOE potential instead of the PRE
module is that all the esim functionality is available for ensemble simulations,
otherwise I would have had to look more closely into using the method
of Iwahara et al.(his scripts are in the python examples) to refine
ensembles of structures. There may be some simple clever way to do all
this that I'm missing which would make it a non-problem in practice.
David Lowry
----- Original Message -----
Sent: Tuesday, August 15, 2006 1:47
PM
Subject: Re: Speaking of custom energy
terms...
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SUSAN VARNUM <[EMAIL PROTECTED]> wrote:
>
I've noticed two examples in the literature where folks have used step
>
potentials rather than "square well" potentials for some of ther
>
restraints. Is there an easy way to convert the NOE restraint from
>
square to step? I've been using an ad-hoc solution of setting
the
> upper bound to 99 angstroms but this is only good for proteins
with
> extended chains that do not exceed this distance. It does
not appear
> that I can use a value larger than 99 angstroms because I
get an error
> message in my out file if I try that.
>
> >
> > With NOE restraint of the form
>
>
> > ( ) ( ) 20.0 0.0
150.0
> >
> > I get, in my .out file
> >
>
> NOEPot:addRestraints: error adding restraint
> >
This is
my mistake- it will be fixed in the next release. However, I
wonder if this
is really a problem in practice?
best
regards--
Charles
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