[gmx-users] The loops run far away

[David]

On Sun, 2005-08-07 at 20:58 -0700, Tanping Li wrote:
> Dear all,
> 
> I am analyzing the interaction between a specific
> residue and close residues. The residue is very close
> to a loop (not the N and C terminal). I solvated the
> protein several times, loops have different positions.
> Sometimes, it goes far away from the crystal
> structures. I tried my best to keep it around the
> crystal position, but I can't. I have struggled for
> two weeks. Any suggestions? I looked through the
> mailing list, but can't find the related information.
> 
You can force it using restraints, but the best method is probably to do
a number of simulations with slightly different starting conditions and
see whether they converge to the same results.

Loops are often mobile of course.

-- 
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
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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