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
anyway.
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.
Tsjerk
On 2/6/07, Mahnam <[EMAIL PROTECTED]> 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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