[gmx-users] fixing protein during energy minimization

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Feb 6 08:56:29 CET 2007

Hi Vabhaf,

Now if you think of following this last suggestion, don't bother.
There's no point in doing EM on a frozen system :D Don't do EM in the
first place then. The reason you want to do EM (and this is where the
manual comes in handy) is to rid the crystal structure of bad
contacts. So you DON'T want it NOT to change (you want it to change,
that is). Besides, your crystal structure didn't include the hydrogens
of your water molecule. So these will have to find a proper position

The thing to do is to just do your EM on the solvated system. No
restraints there. Your structure isn't going to change much anyway,
unless the crystal structure is terribly wrong. After EM, do a
position restraint MD, in which you restrain the positions of the
heavy atoms and of the crystal bound water to the reference structure
(the crystal structure). You can add a reference for PR, using the -r
option in grompp.


On 2/6/07, Mahnam <mahnam at ibb.ut.ac.ir> wrote:
> In God We Trust
> Hello Dear Vaibhav Saraf
>  > My system consists of the protein, water of crystallization and
> > additional water molecules. And before doing the position restraint
> > MD, I wish to perform energy minimization once with the protein and
> > its water of crystallization fixed and only the additional water
> > molecules free. Later would do it un-restrained.
> > So need guidance on whether I can fix the protein (along with its
> > water of crystallisation) during energy minimization
> you can make an index file and make a fix group consists  of number of
> protein and water of crystallisation and then in mdp file define freezegrps
> and freezedim ( Y Y Y ) and with MD integrator.
> Yours truly
> Karim Mahnam
> Institute of  Biochemistry  and  Biophysics (IBB)
> Tehran University
>  P.O.box 13145-1384
> Tehran
> Iran
>  http://www.ibb.ut.ac.ir/
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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