David van der Spoel <[EMAIL PROTECTED]> skrev:
Soren Enemark wrote:
> Hi,
> maybe I am misunderstanding either the manual or the topic.. but - in
> my world -
> I never stop being puzzled by the part of chapt 6 in the manual which
> apparently
> says that such distance constraining is possible even though it (seems)
> to be
> secretly known that it is _not_ possible unless one uses the method
> suggested
> below.
> I believe, I suggest adding a comment in the manual.
>
can you be more specific which part of the manual you mean?
Basically almost anywhere in chapter 6 from 6.1 to 6.25 included.
I mean, pulling works between 2 different molecules, why is it then obvious that constraining doesn't?
> -Soren
>
> */Tsjerk Wassenaar/* skrev:
>
> Hi Kanin,
>
> The only way to get away with that is to merge your two parts to form
> one molecule, with the only connection being a distance_restraint (or
> another bonded term if you want to emulate bond-like behaviour such as
> a salt-bridge).
>
> Best,
>
> Tsjerk
>
> On 9/11/06, kanin wichapong wrote:
> > Dear All
> > I would like to know how to constraint the distance between the
> > different molecule, ex. the ligand and the protein. As far as I know
> > whatever to do the constraint, distance, angle dihedral, it can
> do just in
> > the same molecule.
> > Thank you in advance for all of your help.
> >
> > With Best all regard,
> > Kanin
> >
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>
>
> --
>
> Tsjerk A. Wassenaar, M.Sc.
> Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
> Dept. of Biophysical Chemistry
> University of Groningen
> Nijenborgh 4
> 9747AG Groningen, The Netherlands
> +31 50 363 4336
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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