RE: AMBER: running equilibration

From: Ross Walker <>
Date: Fri, 7 Dec 2007 17:00:15 -0800

Hi Boutheina,
Firstly it is up to you whether you keep the crystallographic waters or not.
Generally if they are exposed to solvent I would remove them. It just makes
things easier in the long run if they have non-standard names for example.
Leap will probably thank you for it. However, if some of them are buried
waters inside active sites for example then you should probably leave these
I think that it should not matter in what order you add the ions since you
need to equilibrate anyway. The advantage of adding them 'before' the water
is that Leap will do it much quicker. You should probably run it through the
ptraj randomizeions command anyway to randomize the locations of the ions.
As for the restraints, 500.0 is too big for MD, it is generally okay for
minimization and is in the tutorial like that but in general you probably
don't want such large restraints. In terms of group input you just specify
the first and last residue of the solute and this will be restrained. So if
you protein has say 250 residues 'before' you add the water etc then you
want residues 1 to 250 to be restrained.
Note, you can also use the restraintmask input these days - see the amber
manual for examples.
something like '!(:WAT | :NA+)' would work - assuming the sodium ions have
the residue name NA+ - you need to check that.
Good luck.

From: [] On Behalf Of
Boutheina Kerkeni
Sent: Friday, December 07, 2007 16:30
Subject: AMBER: running equilibration

Hi Amber users

I have a couple of questions:
1) should I remove or keep crystallographic waters from my PDB file? and add
water using solvateoct
2)Does it matter the order of addions and solvateOct?

I want to run a minimization prior to MD on my protein.
3) I want to minimize all residues except the waters and ions (Na+), how to
specify this in GROUP input?

Hold the Protein fixed
RES, (?, ?)

Thanks for your help

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Received on Sun Dec 09 2007 - 06:07:45 PST
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